Hi John,
I think you have just discovered the reason your proximity switches were disconnected in the first place.
The C10 pull up / pull down unfortunately applies to all input pins and adding a resistor will not solve the problem.
As I see it you could either.........
1) Do a bit of sugery on the BoB to remove the pull up resistor which is associated with the pin you use for the estop or possibly.........
2) Swap the estop switch from one with normally closed contacts to one with normally open contacts and reconfigure your active hi / low within Mach (incidentally I use normally open contacts on my estop and limits).
Given the choice I think I would go for the surgery but then electronics is my thing.
Tweakie.