Yes, that's normal. After using fix/perm kits, cells appear much lower on FSC/SSC plots. I don't think there's a way to prevent it.

Yes, it's totally normal and doesn't affect the data or analysis downstream. Though you do need to ensure that all single stain controls (both cells and beads) are subjected to the same process. As the fix/perm treatment can affect the fluorescence profile of certain fluorochromes.

It is normal to see altered profile on FSC afterbusing fixperm buffer. Gate the population and see how much signal of interest is being captured