I would conclude that you have probably already resolved this question by this late date in July however, I will toss in my 2 cents for anyone that might benefit.
It might seem simplistic but I would try reversing the two batteries and see what the behavior of the one that never seems to fully charge alone is.
I would also get another known good battery and try it alone and see if it does the same as your problem child did in the main battery bay. See what the lower rated battery does alone in the primary battery bay does. I don't think the solution is in the rating of the battery however.
If there is no change I would live with it by doing as you have to resolve the problem or pay a big troubleshooting bill.
As far as the 5200 mAh battery goes. I don't think you will have any problem with it as far as compatibility goes. If your charging circuits are "gummed" up then you, again, should use the scenario that works as you mentioned.
Talking about “gummed up”, you might also make sure your battery contacts on the battery and computer are clean and tight!
I have a C640 and am purchasing two 5200 mAh batteries, one for each bay. After a long chat with Dell they confirmed that there is no difference between the main battery and the secondary battery. They simply are labeled primary and secondary with unique part numbers apparently since some Latitudes have different physical fits in the secondaries which is not the case in the C640. The electronics of each battery is the same according to them.