AAAAAAHHHHHHHHHHHHHH I SEE...
THATS PROPPA OLD SKOOL!!!!! oh the xr3 memorys!!!
this is what was used before rca outs were common on head units!!
so you have attached these to ya rear speaker outs of your head unit, then plugged the rca from that to ya amp correct?? (which is the correct way)
in which case, i would say the same sinario i suggested as b4, as you have turned it up, the resistance on the speaker out from head unit has caused it to throw hissy fit! (if you say it does this when you disconnect the crossover)
or
you have a dodgy earth..
or
there is a fault within the Xover which has inturn messed up your amp, aka your rca inputs, (these are very sensative to the correct impedence)
or
there is bare wire touching metel somewhere (maybe on the cage of ya head unit or in dash, are ya speaker connections insulated?)
the sub is pulsing because it it picking up power from somewhere that is not stable...(or a disterbance in power delivery,) like a serge of power going on then off again but really quickly??? if so that says to me a power sorce (amplification of some sort) is goin ape sh1t some were along the line. it could even be "bleeding" which is where 1 power sorce bleeds into another, (e.g like if your listning to radio at home and you turn on a light the radio wick "pop/ click) same princable.
i would suggest wiring just speakers to you head unit and if you have the pulsing then you know its ya head unit. if not ad ya amp and see if it pulses, so on & so on. do the same with all componants until eventually you will add something that causes the problem.
questions,
what head unit have you got?? does it not have a pre- out? (RCA out)
are your cables balanced, sheilded, even directional?? cheak your rca lead aint got arrows on it, i have had "directional" rca`s b4, never plugged em in the wrong way round but ya never know! (If there sheilded you wont have "bleeding")
have you tryed unbridgeing your sub to see if pulseing stops?
also i noticed you say you powered the Xover.. these are powered purly my the M.A`s of power that run through your speaker cable.