[Q] Link2SD problem on SG S2 topic

I have been using OmniROM KitKat on my Galaxy S2 for a while with no problems. I've recently had a GPS issue (still don't know the cause but that's another issue for another day) so decided to update my ROM to the latest nightly. The update went well, but then I found that I could not access any of my apps that had been copied using Link2SD.

I had created an EXT3 partition on my SD card and linked all files onto there using Link2SD. It had been working perfectly before but the update had obviously changed something in my system. When I run Link2SD, I get the following message:
mount: Device or resource busy

Googling this it looks like the partition is already mounted (a2sd?) or some scripts are missing. (Link2SD still has root permissions) I've had a look in init.d but can't see anything remiss, though I'm moving out of my comfort zone here.

Can anyone tell me what I should do next? Do I need to delete and recreate the EXT3 partition, copying the data back on to it? Would uninstalling and reinstalling Link2SD help, or would that cause even more trouble?

Finally, if I do another ROM update, what should I do to stop this happening again?

Thanks for your help.