Yes, it happens to me quite often, I even posted a question about it awhile ago: http://www.ironcad.com/support/community/index.php?showtopic=872 , and at the time seemed like I was the only one. Here is the text of my prev. posting:
"Please bear with me:
I have a scanned image I apply as texture in smart paint dialog box. I use "natural" setting, it goes on as 1,1 ratio, and everything is fine. Next, I add a hole shape. This action for no apparent reason changes the smart paint scale, and I have to use now a 7,3 ratio to get the same look. I do that. Then, I change something about the part, let's say, add a blend. Whops, now it changes the scale back to the original, and my part looks like it's made of several blocks. I have to go back to smart paint and change scaling ratio to 1,1. Annoying."
Does this look similar to your problem?
Alex.