To reproduce:
create a block 1*2*1. Using the 'select texture' tool select one of the rectangular sides (non square). Set the U and V scaling to different numbers, say 2 and 4 respectively. Now rotate the texture 90 degrees. The texture will be distorted (stretched) because U and V got rotated with the texutre, but didn't change. That may be fine. Now go and change the 'Repeats per Meter' to 1 and click apply. The texture will be stretched, because it is still setting the U and V as if the texture isn't rotated. This should be fixed.
At 90 degrees all I had to do was go and swap the U and V values. I know a full fix for all angles may involve a lot of funky math, and I don't really wanna do it, but it seems and 90 degree and -90 degree rotations are common enough to warrant a 'quick fix' that recognises those angles and handles 'Repeats per meter' currectly.
Sub-question: Which is better, posting something like this here or with the bug report tool ingame, or both?