I think it may be related to the new bootloader (Optiboot) used in the 0023 & 1.0 IDEs for the Uno. I don't know for sure, but like you I don't remember having the problem or using a diode there until recently.
I'm not sure about the diode choice. I'm definitely a neophyte with circuits so in my designs I've just been using the S01575; it's cheap from Mouser ($0.06 ea) so I didn't put a lot of thought into it.
Hope this helps,
Chris