I've wondered the same thing, but I doubt you'll find the answer that you seek on this forum. Here's my best shot at a solid, scientifically-founded answer to your question:
To understand the effects of aging a bourbon beer, you need to know two things: the key flavor and aroma compounds in whiskey, and the effects of age on these specific compounds.
The chemicals that give bourbon it's characteristic taste are numerous and varied. Whiskey is a complex mix of esters, aldehydes, fatty acids, phenols, and alcohols. Probably the most significant flavor compounds are the phenols from the peat, which impart whiskey's characteristic smoky flavor, and vanillin, the phenolic aldehyde that gives bourbon it's distinct sweet vanilla flavor. Esters also are a large contributor to whiskey flavor, as are melanoidins, and various other aromatic aldehydes.
Some compounds decrease with time, as Denny mentioned. Other compounds, though, like aldehydes will actually increase. For instance, phenylacetaldehyde levels can increase by a factor of ten in a beer aged for a few years.
Over time, phenols will readily oxidize. Esters will too, although levels of some esters, like isoamyl acetate, will decrease, while levels of other esters can actually increase. (This is why some beers become more whiskey-like over time - increases of esters that taste like whiskey.) Aldehydes, which have a massive range of flavors from grassy to cinnamon to Maraschino cherry, tend to increase with time.
The consequence of this is that beer, with or without bourbon, undergoes many flavor changes over time. Whiskey itself changes, but it is much less volatile than beer. So if the beer did change over time, it was probably due more to the beer changing than degradation of the bourbon, although there are a lot of commonalities in the chemical reactions. Your question was probably more of a general discussion point, but the topic is vastly complex and deep.
I'm gonna also throw out there the possibility that your buddies' perception and memory might be more of the culprit for the tasting difference - that is, they could have easily remember the beer being better than it actually was, or been slightly drunk and happy to be at a brewery when they tasted it, and overglorified it, etc.
Anyway, here's a link to a review of a paper that is relevant. Maybe you'll find this interesting:
http://beersensoryscience.wordpress.com/2010/11/15/chemistry-of-beer-aging/
