I have no experience of your boiler but a lifetime of suffering poor connections with electrical and electronic equipment. Your 99% certainty about the timer module suggests a dry joint or a poor connection of some sort with the wiring. Tapping gently on the suspected parts with a wooden spoon might get you close to the problem.
If you can inspect the control board you may find a dry joint (or several) and if you're confident with a soldering iron might save yourself £60 - if you're not sure how to recognise a dry joint Google Images Dry Joint has plenty of examples.
Good luck...
Peccavi
May 2009