Off topic, I have 5 machines in the farm running Suse 9.0, MD 9.2, Knoppix... More at the office.
At to your issue, I haven't seen that one, but I would check the PATH.
I would also do the usual scans with HOUSECALL, Adaware, Spybot and CWSHREDDER to make sure that a pest hasn't slipped in.
I'm a pc tech and have seen alot of weird windows problems but not this one. After typing a command, for instance msconfig, notepad or any other program, into the run box the program runs fine except a message box appears stating windows can't find the command I typed in. Click OK, the box disappears and the program continues to run normally. When launching the same program from an icon this does not occur. Only when entered in the run box. I realize this isn't much of a problem, especially for users that never ever type anything except maybe into a word processor (most people are mouse-centirc these days but I'm a Linux devotee and am at a command prompt very frequently). I feel the solution is a simple registry hack but reaaly don't know where to look. Any ideas? TIA