What do you mean by "Merging the two 4.3 branches"? Do you merge the changes from one branch to the other? Or do you merge the changes from both branches to a third branch?
Please note that when merging (specific revisions from) a branch X into another branch Y, only the changes made in branch X itself are merged, not changes to the branch it was created from.
An example. Say you create 'branch-1' from the main line and commit revisions 42 and 43 in it. Then you create 'branch-1a' from 'branch-1', which becomes revision 44. Then you commit revisions 45 and 46 into 'branch-1a'. If you now merge 'branch-1a' to the main line, only the changes made in revisions 45 and 46 are merged back into the main line and not those of revisions 42 and 43, because they were not created in 'branch-1a' but in 'branch-1'.
So if you are merging the changes made in one 4.3 branch to the other one, or even all changes of both 4.3 branches to another branch, you are still missing the changes made in the "parent" branches.
Under the hood, the Modeler uses Subversion to implement version control. See this stackoverflow question for some good tutorials on branching and merging with Subversion.