Assuming you’re simply getting the warnings mentioned in the title for this topic, I think it’s probably safe to ignore them – but I would recommend you make sure the commands are using the sform rather than the qform (you can set that in the config file, as mentioned earlier in this topic).
The reason it’s probably nothing to worry about is that the qform is a bit unstable (see discussion above), and that will introduce some rounding errors between the qform and sform that can trigger the warning. In your case, you can see from the fslhd output that there are minor differences in precision, but that’s really nothing to worry about as such.
On top of that, there was a bug in the code that performs these checks, making it quite likely that you’re being warned by mistake… This has been fixed in 3.0.2.