I had been having the same problem since upgrading to Lion (as you can see my latest post). I have two Macs here at my office (one on Lion and one on Snow Leopard) with a local Time Capsule and a remote Time Capsule across town (for back ups).
When I upgraded the one Mac to Lion I could no longer see the remote Time Capsule and the local Time Capsule said I needed to re login to BTMM using iCloud to restore functionality. I did that and the Lion Mac was happy with that TC, however it could still not connect to the remote TC. The other Mac with Snow Leopard can connect to both the local and remote TCs no problem.
So, there seems to be a significant difference between BTMM for MobileMe and iCloud. But how to I re-establish connection to my remote TC without physically relocating it to my local network when just about any help or troubleshoting always seems to begin with:
How to set up your Time Capsule or 802.11n-based AirPort base station for Back to My Mac
Make sure you are on the same local area network as the Time Capsule or 802.11n-based AirPort base station that you wish to configure.
I wouldn't think I'd have to do that just for a LOCAL OS upgrade.
BTW: All software and firmware are current and upgraded.
Regards,
Scott