Dear Sarah,
I have seen this 'is not a valid integer' at quite a few practices with EMIS lately, I've requested EMIS to let me know what this means and how this could be prevented with future practices, but as you say they don't seem to know what's causing this.
I found that the only way they can fix this is by doing a total re-install of the interop config file on EMIS (this shouldn't take too long). The quickest this problem was resolved at a practice for me was within 20mins, and the longest it took (so far) was about 2hrs.
If/when I hear back from EMIS as to a resolution, I shall post it here.
Many thanks,
Nico
Sunquest - Implementation Specialist.