Regarding CDs that cannot be ripped, there must be something specific about those discs that have an added layer that is interfering somehow. If you let me know the catalogue numbers of this discs i might be able to discover the cause, but either way I might not be able to provide much of a solution.
In terms of FLAC files, there are different levels of compression that can be applied, so not all FLAC files are quite equal in that sense. As @DanCollier says, we use the absolute least amount of compression possible when ripping CDs, whereas you might find that CD ripping software used on a PC used a much more aggressive amount of compression to save space.
This does not actually change the audio data itself when decompressed, the problem is that the harder a system has to work to decompress a file for playback, the more this process in itself can introduce an element of noise. This is why we use the very bare minimum of compression when ripping in FLAC.
Is the FLAC compression level "0" when ripping in fast mode?
What is the FLAC compression level when ripping in quiet mode?
Thank you.