Hi, I know it's been a while since you posted this but I just wanted to say you are not the only one who has this problem with Nebido. I have been on Nebido for around 2 years and before that I had been on Testogel for approximately 6 months. Whilst my periods stopped just before i started Nebido, I still occasionaly get a random bit of cramping. Touch wood nothing so far has ever come from any of the cramping, (other than the annoying pain).
You need to remember that the testosterone is what is making your periods stop and it is what is effectively making you infertile. However just because you are infertile does not mean you are sterile. Your ovaries and your internal sexual organs are technically still working just not in the same way they used to before T. This could be why you get the cramps occasionally, almost like a phantom period; no blood, no eggs, just your body still trying to do something which it cant do.
However it also could be your testosterone level. If you have too much testosterone in your body it does convert itself into oestrogen. I would recommend trying to get a blood test arranged for that six week/ middle point in between your Nebido injections so that your doctor can look at your blood results and have a look at your hormone levels. I would also suggest bringing this issue up with both your general GP and your Gender Clinic Doctor. Your doctor at the Gender Clinic should have more knowledge and helpful information than your normal GP.
If you are still having issues with Charing Cross I would suggest trying to contact a different Gender Clinic. I am unsure of your location but the ones further out from London are often more easier to communicate with and they will see you regularly every 3 or 6 months. Please note that for different Clinics you would need to be referred again which might be a bit of a ballache. With Charing Cross try calling them at varying points in the day, you never know you might get lucky; also have a look if there is a contact email address as you mgiht have a bit of luck then.
As for the cramping, pain killers and sleep untill they take effect. Not much can be done I'm afraid, but least you know that you are not the only one