Think I might have found a working solution to this problem in RTW v1.3 after a few tests. Note that this is when you have at least two generals commanding separate armies, IE one heading the assaulting / defending army, the other general heading the reinforcing army:
* When the reinforcement check-box appears, uncheck it.
* Now right-click your opponents army banners to observe what you're up against (if he has multiple armies, study them all).
* Close the opposition army scrolls.
* The check-box should now either be unchecked or rechecked.
* If the check-box is checked, do the following:-
+Uncheck box
+Recheck box
+Uncheck box
* If the check-box is unchecked, do the following:-
+Check box
+Uncheck box
+Check box
+Uncheck box
All you are doing is checking / unchecking the check box at least twice, this has appeared to solve the problem for myself at least. Haven't got a copy of BI installed, so haven't tested it on this.
Now when you enter the battlefield and your reinforcements are called upon, you should be given complete control of every unit in the reinforcing army, including the general heading it. You can also have more than one general in both the main army, and also the reinforcing army.
Note that this was done for several consecutive (or over the space of a few) turns, where reinforcements were used in a battle. Let me know if this potential solution works for you.
[EDIT:]Various screenshots added.
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