Not sure what you mean by "I have the pins set to jog off limits".
There is a setting on the Settings page which is Auto Limit Override, if you have that chosen then when you hit a limit you can just press the reset and jog off the limit. However you shouldnt really need that if you set up softlimits as they will prevent you from hitting the hard limits in the first instance. The only time you would hit them is if you lost steps for some reason and Mach thought the table was somewhere other than where it is.
Hood