I am not a tuner but I do know a couple of things that might help:
1. The PCM Code is the four alpha/numeric code on the label attached to the PCM box. The PCM Code identifies the base computer software.
2. The strategy code is the software/firmware revision number of the PCM Code.
3. There is also an eQuizzer Code that performs a checksum of the PCM code and if it is inconsistent the car goes into a "no start" condition.
4. When a dealer re-flashes the PCM (depending on the latest revisions) it effects any of several control modules within the PCM software - fuel injection, EGR, Transmission control units, etc. - and updates the Strategy Code to the latest revision number.
5. A handheld tuner does not effect the PCM, only specific parameters in the currently loaded strategy. A handheld tuner does not change the Strategy Code number.
Given the above, it seems that if your car is in a "no start" condition then the eQuizzer Code is inconsistent with the PCM Code. I think this might happen if you changed from say an auto to manual tranny and changed out the PCM box and loaded your modified tuner software.
As for the Strategy Code, that of course can be read via the handheld tuner. Oftentimes, the Tuner/Programmer will ask your for the PCM Code on the box so that he can check that the Strategy Code is in-fact a revision of the base software.
So, if we agree that the handheld tuner updates only certain parameters of the strategy and your Tuner's first tune loads and unloads fine, then there is an issue with the Strategy Code revision of the second tune. If your Tuner simply made a copy of the your first tune and modified that, then I don't see how there should be a problem loading either one. I would start by asking your Tuner this question and move on from there.
Just my .02, I could be wrong.