Is it a behavioral problem or a genetic problem.

My cat - an abandoned stray - is truely lovable towards me in the middle of the
night and first thing in the morning. We always thought she hated my husband
and all men (as displayed by her action of running out of the door and away to
hide everytime) but today I was with her in the morning and left her to go out
for the day. But I left my wallet at home so I turned back and quietly walked
into the house so as not to disturb her sleep. When she heard me she quickly
woke up , dashed to the petdoor in fear and never gave my voice or my presence
a chance. I kept calling her in the reassuring voice she is familiar with but
to no avail. She treated me like a stranger and she hides from all strangers.

Question: I know she probably has a history but it doesn't seem right that she
even behaves like this towards me whom she recognises as her carer, feeder and
keeper. Its like a switch that goes off in her brain. Could this be a genetic
inbreeding problem???Or a behavioral modification matter which could be
resolved in time.