Well, nothing is really in focus in the Baader-U image, so I seriously doubt that it has anything to do with IR leakage.
Knowing the Meritar and its weaknesses, I would not seriously consider it a good lens to test out the abilities of filters, especially since it is then hard to judge what was caused by the lens and what by the filters. An old engineering rule is that a measuring tool should be at least 10 times better than what is measured...
Oh, and there you have the answer within your text: "The focus was not altered between the Baader U and the Neptune U." So using a lens that has focus shift and knowing that the Neptune-U has about a 15nm shift of its transmission center wavelength as compared to the Baader-U, would clearly mean a decent focus shift between the two shots. I would recommend to re-shoot and at least focus individually.
Further, it is mentioned that the Neptune-U needs 2/3 stops more for reaching the same exposure. This implies that the filter with shorter center wavelength and/or lesser transmission (didn't you want to show the measured transmission spectra?) causes that - but it is neither, is is the substantially decreasing UV transmission of the used Meritar lens at shorter wavelengths that causes that. So again, I seriously doubt that this lens is an appropriate enough tool to show the capabilities of your new filter!
Edited by kds315, 29 June 2012 - 19:56 .