CAT-6E Question.

Some non-data transmissions over Cat6 have shorter allowable distances than over Cat5e.  VGA, DVI, video externders won't go as far over Cat6 wiring.  The increased skew will smear the colors at the receiving end.  Sometimes as much as half the distance over Cat6 versus Cat5.  Different twists are great for NEXT (near end cross talk) reduction, but cause timing problems when the signal must be re-combined at the receiving end.

All of your data networking hardware should be fine.  Both Cat5e and Cat6 allow ~90-100m max end-to-end, and Cat6 is physically compatible with Cat5 & 5E connectors.

I don't certify my cable.  The hardware and the service is expensive if you are paying a contractor.  For my recent installs I use the CableIQ Qualifier from Fluke.  It's a fraction of the price.  I don't need printed certifications...no service contracts or installation contract requirements.  All of those come at a much higher cost.  Don't get me wrong..it is a valid point to consider for your infrastructure...one that could last 10+ years.  But "qualifying" or verifying gigabit compatibility was sufficient for my needs.  I didn't need the more technical specifications involved in a true certification.

But the average office install does not use 10Gb, not even in the server closet or backbone.  That is where the Cat6E certification is supposed to shine.  Even a tech savvy office running gigabit to the desktop has OS and NIC issues to deal with before looking at Hz sweeps.

Also, as 'exp' stated, buy the proper components.  If you do not have all Cat6E rated patch panels, patch cords, and RJ45 jacks, you've just wasted a ton of money on 6E cable.  You have no higher rating than if you had installed 5E and bought faster equipment.  The lowest rated component is the standard.  

Then, you have to deal with the installers.  Was your 6E cable and terminations installed by an electrician or regular low-voltage contractor?  General contractor?  I've seen cables stressed far beyond 15-20 pounds of force.  Less than 4" (even less than 2") radius bends.  Nicked sheathing.  Nicked wire insulation.  Staples.  Parallel runs with high voltage.

The 6E label will not overcome any of those problems.

(On the strength of one link in the cable dependeth the might of the chain...)