Penny - I don't have any particularly useful advice - but I can comisserate!

What I've noticed, is that this guilt-reflex happens mostly in setting boundaries with my foo. Other people, not so much. I call it a guilt-reflex, because of course I got habitually programmed to show/feel the appropriate guilt -- whenever I wasn't throwing myself under the bus for my mom or bro. I'm thinking this is one way I was kept "playing my role" in the dysfunctional loop-de-loop. Kind of an emotional blackmail club. Beat her with guilt... so she gives in and does what we want.
It hits me worst, when it's just something little... a thing that happens a lot with "normal" people and is no big deal - with normal people. And I think some of it... is the flip-side of the guilt reflex... my foo ain't normal... so it's as if they have "special status/access" to me -- and because they're "special" the normal boundaries should not apply. So, I end up protecting the people who would have me stay feeling guilty about not anticipating their every need and always, always dropping whatever I'm doing to care for them.
This is a kind toxic guilt, I guess (for want of another word to differentiate from guilt that arises from trespassing someone else's boundaries, or doing something "wrong"). The feeling of guilt has been manipulated to control us -- and allow the foo to continue denying us our boundaries - to perpetuate the need THEY have for enmeshment. The guilt-reflex only sets in on me with FOO; other people who do the same thing invoke anger from me.
As far as I know - what Hops said is the only way to get past it; just keep setting, maintaining your boundaries. If a guilt-reflex pops up - talk it through with someone. I have to check with hubs sometimes, to see if he thinks my feeling is appropriate; if it fits the scenario. Then just endure it (but don't change your boundary!)... and let it go. You're breaking a programmed response and the only thing I know of that can replace one response with another is repetition.