Indexed color and transparency in PNGs

I'm working with a software developer who is revising his subtitle rendering application to meet my company's specifications. The renderer produces an image sequence, and we agreed on using PNGs with a transparent background as the format for the image sequence. The renderer is producing PNGs in Indexed Color mode, so Photoshop and Windows Photo Viewer recognize the transparent background, but Premiere Pro CS5.5 and CS6 don't. I can re-save one of the PNGs after switching it to RGB mode in Photoshop, and then Premiere Pro recognizes the transparency. I'm not surprised by any of that. What I am surprised by is that the software developer says he can import the same PNGs, without switching to RGB mode, into his copy of Premiere Pro CS3, and Premiere recognizes the transparency.
Is there anything I can do besides batch processing in Photoshop to get Premiere Pro CS5.5 or 6 to recognize the transparency in an Indexed Color PNG? Has something changed since CS3? I did look under Modify>Interpret Footage to make sure that my Ignore Alpha Channel box is unchecked for the PNGs, but I can't find another relevant setting to check, and I can't figure out why CS3 would be able to recognize an Indexed Color PNG.

PNG's need to be RGB.
CS3 was a long time ago..
You can however import gif in indexed color with transparancy.

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