=Why on earth would an extension cable stop only the desktop from booting when used in card slot number 1?
Not sure if this is your issue or not, but if by saying card slot #1 you actually mean the first card slot (number zero) then the bios might be misidentifying the card as a bootable network card, waiting for it to initialize.
Keeping the same slot and switching the one "cable from hell" changes my results, so I doubt this is the case.
High speed signals require great care.
Proper transmission requires traces with the proper impedance and a minimum of discontinuities in the signal path. Each discontinuity (connectors, pins, etc) will pass most of the signal, but a small portion will be reflected backward toward the source. The bigger the discontinuity, the larger the reflection.
Normally, your traces are relatively short on the motherboard and these reflections will reach the source before the next symbol (think 'bit' in this case) is transmitted. When you extend the trace length as far as you have, it is entirely possible that the reflections take so long to reach the source that they're overlapping on the next symbol (bit). This is called inter-symbol interference (ISI).
So why does it only happen in slot 1? My guess is that this slot has either the longest traces, or a slightly different impedance that causes a larger discontinuity when you connect your extender contraption.
The solution is to not double up your extenders. If you must extend something that far, use a single extender.
Edit: Note that when I say impedance, I'm not referring to just resistance. The complex impedance of a transmission line or lumped element refers to how it interacts with a time-varying signal. It's not the same quantity that you can measure with your multimeter.