If you have applied replaygain to your FLAC files then the volume gets automatically normalized by foobar, i.e. it goes up or down as required. That's why you are hearing a difference. It has absolutely nothing to do with compression. It's nothing to worry about. Replaygain just consists of tags added to the FLAC metadata that tells foobar how much to adjust the volume. If you don't want replaygain, go into foobar and turn it off.

Here's some info: http://en.wikipedia.org/wiki/Replaygain