Hi Jon,
I don't recall changes to 3drotate that would cause such a problem. Are you absolutely sure that the command line used in the past is the same as the one used now ? If you still have the data sets that were rotated in the past, you could use 3dinfo to examine their history and make sure the commands are identical.
If you have the old data and find the commands identical then I suggest you send me a sample of the original data, rotated data with the old program and I'll try to find the problem.
cheers,
-z
