In 3 different files now I've had colors assigned to various elements. I'm thinking that at least some of the elements were set using the Filters > Adjust Color > Brightness/Contrast, so they would be bitmaps after the change. When I return to the file, the colors are changed and it's impossible to change them back to the color they are supposed to be. I would expect I wouldn't be able to change the bitmap color, but I would also expect that the color would not be able to change between the time I saved and closed the program and reopened it. And it's not slight color changes. I'm talking it was dark blue when I saved, and it's dark red when I open in. I'm also not able to change the color on non-bitmap elements.
Today I also had the problem of an inner glow setting gone when I opened a file. I'm feeling like I need to resort to writing down all my colors and filter settings before closing a file, but that shouldn't be necessary!