I did not run the scenario because I don't have all the addons required but I did have a look at it (the scenario on post #1204) and the scenarios before that.
The only thing that stands out is the Hermes XR5 and its payloadbay. (Actually, it's just the Hermes because correcting it will automatically correct the payloadbay as well).
The Hermes is flying away from the sun at 2.93 AU/s (!?) and it's at a distance of about 113.9 AU, so I am guessing that's not what you want.
What was its state in the scenario before that?
I looked at sorindafabico's scenario on post #1183 but there are even more ships in a weird state (Mir, SH-03 and Hermes+Payloadbay).
Tracking it even farther back, the problem persists on SolarLiner's scenario on post #1174 (Mir, SH-03 Chronus and Hermes+Payloadbays) and exactly the same ships have the same problem on Tmac's post #1160 and SolarLiner's scenario on post #1148
All the weird states on these ships (Mir, SH-03, Chronus and Hermes) seem to have first appeared
after Felipi1205's scenario on post #1144 where all the ships that are affected from there on are landed on Earth.(except Mir)
The problems seem to have begun to occur when you first used
Code:
BEGIN_RealTime
TIME=xxxxx.xxxxxx
END
in the scenarios, between post #1144 and #1148.
If the ships in question have not been used since Felipi1205's scenario on post #1144, you can get their state from there and copy it on the latest scenario. Then deactivate the realtime addon and try one flight to see if that was the problem.
Hope this helps