Indeed there's something fishy here because no 'flipping' should occur during import by default. Depending on how you assign the columns before loading an ASCII file you could get a non direct basis (mathematically speaking) and then observe a 'flipping' but once it's fixed you shouldn't see it again when you load the resulting cloud...
Can you share a sample file with me? (email: cloudcompare[at]danielgm.net). Or at least post snapshots of the various dialogs that CC displays prompts while loading? (especially the 'global shift' related ones).
Opening File
Re: Opening File
Daniel, CloudCompare admin