Issue with my filenaming in Lighroom

My workflow is to use Downloader Pro to rename my raw files in injest from the card. They all get a date_time_sequence_camera_myinitials name.

ex. 061020_1530_2654_1D2_JS.CR2

Those that are worth working on go into photoshop. I save a master file with layers with the exact same name as a psd file.

ex. 061020_1530_2654_1D2_JS.psd

I also save a flattened and sharpend print version adding the paper size to the name as a tiff file.

ex. 061020_1530_2654_1D2_JSltr.TIF

Now for the problem, When I import these into lightroom, it seems to have an issue with the CR2 and psd files having the same name and only imports the psd file.

Anyone know if this is on purpose?

PS: I'm going to post this in a couple of different places so I'm sorry if you've seen this already