No issues here either. I can switch between different keyboards and it stays as selected. I'm still on 4.1.1, but it shouldn't make a difference. Btw, with Swiftkey they always recommend to uninstall an old version, even offer that as one of the options in their setup. Furthermore, make sure you are not running a beta version of their keyboard (in case if it got disabled). For example, they had a free beta of Flow which stops working after expiration date even so it's still available to select from the list. Also, if you installed or updated to a new version of Swiftkey or another keyboard, don't assume it will work by default even if selected. Click on its icon/shortcut and run through setup/config.
Oh, and did I mention - I LOVE the latest Swiftkey with integrated FLOW!!! Not just an accuracy of spellchecker and Swype (still mind boggling to me how they get it), but an amazing prediction of typical phrase patterns. In some occasions, I swype the first word and than just "type" by selecting the next suggested word. Hands down, the best keyboard for one handed typing which is very important with such a big phone. Plus, you do get Split layout in landscape.
ONE very important thing, do you have an external keyboard plugged into your GN2, through OTG cable? If you do, it ALWAYS switches to default Sammy keyboard, no matter what other keyboard you have selected.