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Would the wires you have replaced happen to have 9013 and 9012 written on them at intervals? If so these are CAN Bus wires. They are a set length and the same length as each other.
The only common thing with all of the problems you have mentioned is the BSI (in car?) and the BSM (under bonnet?). i suspect it will be the BSI as these units have been known to cause problems although it could also be the BSM.
I would suspect if you had appropriate diagnostic software then there may be some fault codes listed related to BSI. As far as I know these units require programming to the vehicle so you would have to take the vehicle to a dealer for this.