That could be the issue.
Why would you think that?
Maybe they have different resistance? (The lower the resistance the more output you get and that will drain the battery more)
I can think that your old batteries got a high resistance over the time and the new batteries have a low resistance. The new batteries will drain faster and the pack gets unbalanced.
I am just speculate. Would be nice if somebody could verify my words. 
When I added the extra cells, I added a new one to each 3p pack so this sorta thing shouldn’t really be an issue. As I mentioned though, the issue turned out to be a result of a couple of the fuse wires breaking 