I thought I had posted this.... But it hasn't appeared.
Currently we have WHMCS 5.3.14 installed, and saw an update for 6.1.1 so I thought I would do that.
It failed, it seems it just stopped during the database upgrade process and then the page timed out. We are running on a Cpanel Centos 6.7 server running PHP 5.4.4. Reseller Club Mods "RC & LB Tools v2" is installed (Which I like). Apart from that there are no mods to WHMCS and I was about to apply some but thought I would upgrade first.
I then went back to a backup, clearing out my public_html directory and database so my system now works albeit on an outdated WHMCS.
Some googling indicated that sql_mode being strict may be a problem. I checked and sql_mode is an empty string. Is there a special SQL command I need to run first?