Intonation issues with Yamaha FG3 / FGX3?

I have seen several people on multiple forums complain about intonation issues on Yamaha Red Label FG3’s and FG5’s. People say that this occurs when using a capo.

Anyone here play a Red Label Yamaha? Any intonation issues?

I’m thinking about trading in my Guild D140 for an FG3 (love my Guild, but I find the neck a bit more comfortable on the FG3) if I did end up having intonation issues while using capo’s is there a way I could fix this? Could a good set up fix this potential problem? Or is it possibly something more severe?