Hi,
I was looking at the schematic:
https://s3.amazonaws.com/digispark/DigisparkSchematicFinal.pdfand noticed the Schottky Diode D3 is drawn backwards (and Eriks name is misspelled)...
anyway, If the pull-up resistor R3 was connected on the USB side of D3 (anode), it would only get power when the device was plugged to an USB port, so it would not interfere as much when the Digispark was powered by external power.
I wonder if the Zener D1 has enough leakage current and/or capacitance to keep the floating PB3 reliably low (or a reliable analog threshold low reading can be made). The idea is that if the Digispark was powered by external power, the bootloader could first read PB3 and if low, go immediately to the user program, otherwise proceed with the 5sec (or possibly longer) delay waiting for programming instructions.
Also, I just got my Digisparks yesterday and I programmed one without any issues (win7-32bit)

Thanks for all your hard-work on this project.