I've had the same problem before.
Whenever you duplicate something with the Ctrl-D supra keys, and apply any SRT to it, if you Ctrl-D again, XSI remembers the last SRT modification and applies it to the newly created object. This is good if you want to create things with repetitive properties, like fence posts, but for some reason, it sometimes copies this information into the duplication properties page so that no matter what object you select from then on, it applies the same SRT modification to it.
It's either a bug or a button you press to activate it, im not sure but it happens.
...I don't know what I just said but I said something...