This is confusing.The cable category of twisted pair wires is determined basically by the twists per inch. Terminated or unterminated they are still cat6 cables. The termination simply determines the use or functionality of the cables, RJ11/14/25 its phone, 45/48 data/Ethernet, and then the rest of the Registered Jack that are all rather specialized can be found here
http://en.wikipedia.org/wiki/Registered_jack
Terminated wrong/different does not change the category of the cable in any way and in fact it is possible to terminate something "wrong" and still get use out of it, just not the intended use, I have seem rather custom punch downs for robotic control at the University of Florida displayed, over a decade ago with cat5 wires and sort of a straight b/bw/o/ow/g/gw/br/brw which is certainly not a typical ethernet punch down., but it was standard RJ45 cubes at the control module, the wires inside were soldered directly to a circuit board however.
The the standard (eight conductors) cable is engineered to function in a "Structured Cabling" system, meaning it is nearly universal for any purpose when implemented properly (i.e., bend radius, pulling tension, bundling restraint ...) terminated properly, and with the use of adapters (i.e., video baseband, HDMI, 327- terminals, 5250 terminals, RS-232, security functions ...).
It is capable of many general use applications as "just plain copper cable" just like any copper multi-conductor cable that is also not used for non-critical, non-category rated purposes (like your robotics project). Different communication protocols use different electrical signaling (T1 versus Ethernet/fast Ethernet/Gig Ethernet versus xDSLx ...) so some are more tolerant of ignorant and/or lazy installers doing things their own way for no good reason (i.e, it takes no additional effort to do it right).
There is far more to "Cat{anything}" than the pair twists. The type of insulation per conductor (which can be different per conductor), the thickness of the insulator per conductor (which can be different per conductor), the overall sheath material, (for Cat6, 6a) the "x" member size and material, the "lay" of one pair to another ... and many other factors.
By terminating the cable {pair},{pair},{pair},{pair} you caused a split pair on pins 3&6 and screwed the crosstalk rating for the cable, especially in full-duplex operation. The spec is established and engineered for all four pair to be terminated in their designated position. Failure to properly implement and terminate will result in sub-optimal performance. The cable may "work" .. you may get a link light (which, at best, establishes continuity and nothing else), but the performance will suffer at some level of signal density.
It is also worthy of note that the "Category" label is merely a method (like "Geranimals")) to permit someone to assemble a segment or span without sophisticated tools and instrument and be likely to have a system that meets the target Category's performance level. That assumes that the installer follow the easy-to-follow directions and guidelines.
The other option is to set up and scan the cabling system with a wide band oscilloscope and sweep generator to plot the overall characteristics of the SYSTEM (cable, panels, connectors, jumpers, keystones, etc).
The short story is "you're wrong" and a cabling system improperly implemented is a waste of money and time. The Category label only applies to properly implemented and terminated systems. All conductors must be terminated properly in the proper hardware for the desired function. Back in the Cat5 days you could buy four and six conductor Category rated cabling. It was engineered to operate as four or six conductor systems for people too stupid to realize what a waste of money that system really was.
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