I believe this is a timeout issue. Because every time I rebuild the last config, saving works at the second time. The difference is, the time spent in the Mechlap, without having saved the changes.
After realising that, I have saved my Mech-Config more often, even if I wasn't completely finished building it. Using this workaround, I never had this bug anymore!
Compared to, having this bug every time after a longer configuration session, I strongly believe this is timeout related.
Edited by Gunhead75, 05 December 2012 - 03:54 PM.