Without being able to observe the problem I cannot be completely certain what it is and what causes it. Thus, I cannot confirm whether creating scripts dynamically will cause the same problem I was referring to.
What I can suggest, is giving upgrading a very quick test - simply change the assemblies and test a page that you know causes this problem. If it does not manifest again, then it is a bug that has been fixed in a later version and upgrading is, most likely, the single option.
It is also possible that this is a false positive - we may be throwing an unnecessary exception, which is then catched. Nevertheless, the DebugDiag tool still catches it and reports it to you. We have had one report about such behavior a few months ago.
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