Laine,
Motor drives create a lot of electromagnetic noise - properly shielding motors and cabling can significantly reduce this - but sometimes filters are needed also.
As for the lowered voltages on your breakpoint outputs - it sounds like you are trying to source too much amperage from the breakpoint line. Voltage will drop from the normal 5v's if this is the case. The spec is:
Output low voltage .................. 0.6 V at 64 mA sink
Output high voltage ................. Totem Pole: 2 V at 16 mA source;
open collector: built-in 3.3 kohm
pull-up to +5 V
(that is from the 735x users manual spec page).
Use a amplifying circuit such as a transistor if you need more current than the specs.
