Yes, I had a similar problem with SME 5.5. I have two USB printers connected, to usb/lp0 and usb/lp1, respectively. Every once in a while, the server swaps them around (I didn't have to reinstall SME to have this "feature" turn on, it did it all by itself after certain printing tasks at least at 4 occassions in the 3 days I had the server running.)
First I could not figure it out as the printers would just stop working and I got weird error messages on my Windows Xp workstations like "The spooler service is not running" and other things, which all resulted in the Windows Xp workstation losing connection with the printers and even (twice) emtying the whole "Printers and Faxes" folder and telling me that there were no printers installed! I had to re-start to make it work again.
I got suspicious when I tried to print on one printer, and the OTHER printer did something (but didn't print as it is a totally different printer and obviously could not interpret the data it received). I solved it by swapping the ports in the Windows printer setup (i.e. assigned my Canon printer to the \server\samsung and my Samsung printer to the \server\canon port...)
Weird, and it looks like something is definitely out of control here...
Otherwise, I have to say that I am VERY impressed by the SME server - this is the first Linux I ever installed (as a test), and I am very likely to replace my Win Xp on my server with SME as soon as I have this printer bug worked out.