Hi Aisling,
I had the exact same problem with a few scans that were keeping me from completing preprocessing in CONN too... the tech had changed the scan size on just a few individuals at only some timepoints.  If methods are helpful for reslicing, here is the method we employed:
In SPM select Coregister (reslice)
Select an image defining space (a single 'good' template image from a normally processing session that has the desired dimensions)
Select the images to reslice (in frames select 1:200 to capture all of your time points, and select all of them from that session to reslice)
If you leave all the defaults, you should have an "r" prefix to the resliced files... if you process those as you normally would, everything should be resolved and CONN will stop getting angry with you.
Just learning this myself, so hope this helps.  
Tray