I was reading this and was going to chime in that you might of had a good base developement that was lacking the development from ass to ground.. now that you are doing that you are hitting an area that you lacked from before... but, narkissos pretty much covered it... Most of the time I prefer to work in pyramid type of structure on squats... when working weight up I do the following.

135 - ass to ground warm up.
225 - ass to ground wam up.
315 - lil lower than parallel... very painful.
405 - close to parallel really heavy depends on how feel.
either go up from here or stay for about 2-3 more sets.
315 - parellel
225 - legs together parallel ass to ground..hits front hard

maybe this can add a variation to work out too.. hits the whole mama jamma.