The human digestive system isn't like a large bucket where everything is digested at the same time.
The following is cribbed (with minor edits) from http://forum.bodybuilding.com/showpost.php?p=1447655 "DIGESTION 101
The order you eat foods in does not make a difference to digestion. Once foods hit your stomach, the peristaltic motion (that is - the muscles in your stomach wall contracting) mix it all together regardless. Also, the different enzymes that are released are released regardless of the order that you eat your food.
In your stomach:-
The presence of food in your stomach stimulates:-
1. Gastrin - this is what is responsible for the eventual release of HCl - or stomach acid.
2. Pepsinogen - this is converted to pepsin by the acid in your stomach. Pepsin is important in the digestion of proteins.
In the small intestine:-
Once food hits the small intestine the pancreas and gall bladder are stimulated:-
1. Pancreas - It secretes many enzymes which help digest proteins, starches and triglycerides (fats).
2. Liver/gall bladder - This is responsible for making and secreting bile. This is important in fat digestion. It is stimulated more when you eat fatty foods. The small intestine itself is also important, but it actually does not secrete anything. It acts to further digest the carbohydrates, proteins and fats, due to enzymes that are bound to the wall of the intestines, and then acts to absorb these things.
So - digestion occurs in two parts - the LUMINAL phase - which involves all of the enzymes that are secreted by the stomach, pancreas and liver. And the MEMBRANOUS phase which is that which occurs because of the enzymes attached to the intestinal wall. It does not matter when you eat carbohydrates or proteins or fats during a meal, because the simple stimulus of food in your digestive tract will cause the secretion of the luminal enzymes (although as you increase your fat, you will stimulate more fat enzymes to be released).
Starches are the only type of carbohydrates to undergo luminal phase of digestion. This results from enzymes (called amylases) that are released from the pancreas. These act to break down the long starches into shorter polysaccharides (intermediate chains called dextrins). These are then cleaved again to form Disaccharides or trisaccharides (such as maltose or maltotriose). Sugars and the trisaccharides and disaccharides from the starches are then further digested in the Membranous phase. This involves enzymes (such as lactase - for the breakdown of lactose, sucrase for the digestion of sucrose and maltase for the breakdown of maltose) that are bound to the intestinal wall. So - these enzymes act on lactose, sucrose and the di and trisaccharides from the breakdown of starch to form glucose, galactose and fructose. These are them absorbed across the intestinal wall and enter the blood to go to the liver. The liver then takes up most of the glucose/galactose and all of the fructose and converts it into glycogen or fats while the rest stays in the blood for the rest of the body.
These are broken down in a similar fashion as carbs.
But - the enzymes involved in protein breakdown are secreted by the stomach (pepsin and chymosin) and the pancreas. There are lots of different enzymes involved in protein breakdown (because of the large variety of amino acids).
So - digestion of proteins begins in the stomach with the secretion of HCl and pepsin which begin to cleave the long protein molecules. This then continues in the small intestines with the secretion of pancreatic enzymes. These smaller chains of amino acids (called peptides) are then either broken down by MEMBRANOUS phase enzymes on the intestine cells to form amino acids or are absorbed as dipeptides or tripeptides and then convert to simple amino acids by the cells. The amino acids are then released into the blood and are taken to the liver. In the liver, some of the amino acids go straight into circulation for the muscles, some are used directly for protein synthesis, but the rest are processed to enter the pathway of energy metabolism, carbohydrate formation or fatty acid formation.
This is a little different. Fat is harder to digest because it does not absorb in the fluids in your gut. The digestion of fat is divided into four stages:-
1. Emulsification - This begins in the stomach and involves the warming and mixing of the fats. This breaks the fats into globules. The bile acids from the liver are then secreted into the intestines and make the fat droplets even smaller.
2. Hydrolysis - Enzymes from the pancreas (lipases) then act on the fats to form smaller molecules.
3. Micelle formation - These smaller molecules (free fatty acids, cholesterol, single chain fats etc) combine with bile to form tiny, droplets called micelles.
4. Absorption - The micelles then attach to the intestinal wall and all the components (except the bile) are then absorbed. These are then packaged (into things called chylomicrons) and secreted by the intestinal cells into tiny tubes in your intestinal wall called lacteals which take the fats straight to your heart, which then enters your back to your heart, which then pumps it to the body. These are then taken up by the liver or the fat cells. These processes in the intestine take a while to complete (depending on what you eat) and so eating one thing 5 minutes after the other will have no effect."
Having said all that, there are certain combinations of food that are less desirable to eat than others, but not for reasons of malabsorption. Don't eat high-GI carbs together with whey, saturated fat or omega-6 fats. High-GI carbs produce a large glucose and insulin response. Whey, saturated fats and omega-6 fats magnify the insulin response. This reduces fat-burning and increases fat-storage. Guess what? Virtually all junk foods are a combination of high-GI carbs and sat & omega-6 fats. The only time that an insulin spike is acceptable is if you have just finished a workout and are bulking (building muscle). That particular insulin spike would be obtained by swallowing whey with glucose or maltodextrin but not fat.
The only other dodgy food combination is fruit and protein. Fruit passes through the GI tract rapidly (possibly due to the fibre and simple sugar content stimulating peristalsis) and if eaten with or just after slow-digesting foods like meat or eggs, results in the protein passing through the small intestine too rapidly resulting in incomplete digestion and subsequent fermentation in the colon, producing smelly farts!