Thanks for the replies.

Unfortunately I don't have a cap for the focusser. However out of curiosity I removed the focusser and looked through the focusser tube and the secondary mirror was perfectly circular (with my eye in the middle

). I guess this is at least a good sign?
Maybe I will try to make a cap with some thick paper. Would it work? something I can then fix to the focusser tube with tape for example, or an elastic band. Then I can make a hole in the middle. I have to go to Sydney tomorrow, but if you think it would work I could try on the weekend.
Due to its construction my scope is not 100% rigid (because of the flexitube) so yes maybe this might be the reason why the secondary mirror didn't appear to be exactly aligned?
Allan, yes, I meant that I "tried" to tighten the screws, but I can't even see their heads and the screwdrivers I used didn't feel right, like nothing (or not much) was happening! They are so far down, that's why it is difficult to do a good job. I have ordered a set of allen wrenches. I should get it in a couple of weeks. Maybe I can do a better job then? They mention allen wrenches in the manual for the screws of the secondary mirror, so hopefully...
Thanks!