Can you share the actual project that you are using? The clock / oscillator configuration would be interesting to look at.
I could (although I'd need to rip out the bulk of the project first). However, this appears not to be a software/project problem, as the same exact design works correctly on the CY8CKIT-143A module, which has the CY8C4248LQI-BL583 (same part I am using).
I'll likely wait until I can get a new board up and running, and see if I have the same issue - that won't happen for a few weeks.
Have a look at the clock screen in the design wide resource (and be sure to double-click on the part with the system clocks to get to the oscillator section). Maybe this can show where this clock comes from.
Took a while, but I got to try out another board and isolate the issue - I thought I'd share this if it would help anyone else.
The answer: a board fault - VSSA was disconnected (floating). Connecting VSSA via rework immediately fixed the issue on both boards - now IMO is 48MHz.
(EDIT: I previously wrote VDDA, not VSSA)