[MC 1.5.1][CC 1.5.2] Turtle dropping things when it shouldn't

I've encountered really weird behavior.
The turtle in question is performing gravel to flint processing. (Place and dig until there is no more gravel.)
When it is emptying it's inventory into the storage chest below it, it also drops the gravel and flint I'm keeping for
comparison. The thing that's bugging me, is that there are no instances of dropping the first slot (my control gravel)
or the second slot all the way empty (my control flint) anywhere that I can see. Yet the first and second slot are being dumped anyways.
This causes problems when I attempt to drop -1 of slot 2 and the program errors out.

Pastebin of the problematic code : http://pastebin.com/C7iya9B7
Gravel in first, flint in second.
Expects block above to be free to place gravel.
Expects storage in the block below.

Thank you for your attention,
~Sora

And now I feel like an idiot. :P/>

Thank you, Cloudy.

~Sora