Hello,
 
When you say that you are getting signal degradation, are you having any specific symptoms with your system? For instance, does the output look fuzzy or something of that nature? Anytime you are using an extension of some sort there will always be some sort of degradation. For instance, Like many video, audio and data cables, HDMI cords can suffer from signal degradation at longer lengths—50 feet is generally considered the maximum reliable length. This is why you rarely see HDMI cables longer than 25 feet.
 
-Jacob B.

Sounds plausible. Longer traces affect circuit impedance and are subject to more EMI. The motherboard manufacturer designed the PCI-E slot and circuitry a certain way. You are modifying their design. Therefore, you take responsibility for unexpected outcomes. A higher error rate lowers bandwidth and causes stutter/jitter. The PCI-E bus is a high speed interface which requires specific signal shapes at specific time windows. Any time the signal integrity is compromised, the PCI-E system will adjust as necessary and performance will be lowered.