Just a thought Geoff, had you cleaed the bike just before you put it away? ive found if i do that that the pads "grabbed" the disc and free off with quiet a bang, first happed on my XJR. I spin the turn the wheels for a couple of days or so now after cleaning. Fine now.
Just one other thing, If youre starting the bike just to warm it up, make sure it does warm up fully. Dont just start it run for a few seconds and shut it down. It floods it/confuses it/ i dont know/ but I did that on my FJR and and had a right game getting it to start next time. The CT is the same, i know cos i did it in Germany this year (TIT!). Its a well known thing in the FJR world.
There is a prededure to get them started again but its scary and can flatten the battery a couple of times.