LED Upload Confirmation Blink

I'm having problems loading a 15,500 byte sketch to my Arduino Mini Pro 328 .
Everything is set up correctly because it will accept and run various versions
of the blink sketch , but no matter what I load I never get the final
confirmation blink from the green LED that comes at the end of the upload . The
arduino IDE tells me the sketches are uploaded with no errors or complaints ,
but no final blink and the large programs I want to run don't do what they should. I can't
tell what the program is doing but the Mini Pro just sits there and blinks
about once every 2 seconds.

I'm trying to upload a sketch for connecting a
Wii Motion Plus for quadcopter stabilization and I have 2 other Arduino's -same
model which will accept and properly run the sketch. Is it possible the flash
memory has somehow been corrupted ? Is there a program to set all the memory
space to 0 or somehow set all the memory to 0 past the point where the sketch
is uploaded ? I don't know much about the technical aspects of uploading a
sketch so any ideas are welcome. Also I would be interested in whether you think
this is a hardware issue - I've done a continuity check between all pinouts and
the 328 chip and they seem to be OK . I've also uploaded the example sketch
to clear EEPROM memory and it seems to work (no final LED upload blink ) but it
gives me a solid green LED when the program runs.
Any suggestions would be appreciated.