I doubt very much that having a different filesystem will effect FlopSwap.
As long as the file system is on the correct partitions it will work.

The reason FAT is recommended is stock Maemo shows the card as corrupt if FAT is not the first partition.

As for the swap at boot issue:-

How are you checking the device is not switching to uSD swap?
Have you modified your booting process or used Ereswap?
With the "Start at boot" option checked, does the file /etc/event.d/relocateswap exist?

The checkbox checks to see if the file /etc/event.d/relocateswap exists. When checked and the dialog closed it installs a copy of the upstart file from /opt/flopswap

At the moment I cannot reproduce any issue.