Our group of three bikes crossed into Cambodia at Hat Lek on Jan 29, 2004. We had no problems leaving Thailand but got stiffed at Cambodia immigration for the visas. We had to pay 1100 baht instead of the required $20 (about 800 baht). No big deal. The customs guys started hassling us about one of our bikes which had no license plate. The guy who owned the bike had been into Cambodia before and eventually convinced them to let us through (about 45 mins of "negotiation"). No money changed hands. However, we were stopped at a second customs station down the road and went through the same process. The customs guys wanted to see a carnet book to stamp even though Cambodia doesn't require a carnet. Another 45 minutes of "negotiation" ensued with more and more senior officials coming down to get an explanation. Eventually, the most senior customs guy waved us through. Crossing into Cambodia cost us 1100 baht and about two hours in total.
We crossed back into Thailand on Feb 4. The process was reasonably straightforward except that the Cambodians made us fill out "vessel of conveyance" forms in duplicate. These are the same forms you'd use if you were crossing with a boat. There were tons of backpackers leaving at the same time, possibly due to concerns about avian flu, so the immigration lines were long. Other than that, we had no problems.