It's difficult to picture what you mean by caulk "bubbling up". A photo would help immensely here.
What kind of caulk? An appropriate caulk for a shower does not get "soft" when exposed to water, nor
does it get "hard" when dry. The application area must be perfectly (perfectly!) dry before caulk application.
The moisture is likely migrating from hairline cracks in the grout/marble above. There is no such thing as a
"permanent" caulk job - it's a maintenance item. Its main function is decorative, and to keep crud from
accumulating in the corners.