winuae.7z now adds hires pixel delay to all color register writes if AGA which seems to "fix" this problem. It was very simple change and has nothing to do with BPLCON1 hires/shres missing feature.
But because this causes quite ugly mismatched borders in some games, it most likely looks like new UAE bug..
EDIT: I guess delay may come from BPLCON4 XOR operation. Because when BPLCON4 is modified, it isn't instant but adds another hires pixel delay (was lores previously in emulation but it is actually extra hires = 1 + 1 hires = 1 lores) before colors change after BPLCON4 modification.
EDIT2: HAM and EHB needs testing, some HAM/EHB bits bypass BPLCON4 so in worst case there are 2 possible delays.. (
http://eab.abime.net/showthread.php?t=85588)