Here's a shot in the dark, but have you tried opening them with the kobo app from a file manager application? That's what I had to do last year in order to sideload any books into Aldiko on my Archos 5 IT(running Android 1.6). In that case, while sideloading was officially spported, Aldiko never found the books I was trying to load, no matter which folder they were in. Thankfully this has not been a problem since I went back to using Aldiko in May. In order to do this, you may need to clear defaults from whichever program typically opens pdfs on your phone. This also only worked in Astro. I tried a couple of other viewers and neither came up with the option of using Aldiko to open a pdf or epub file.
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