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A Flashing CEL is a bad thing. It is emissions related. It could be many things, but with the mileage on your car, it may well be that the O2 sensors are going Kaput (they're only rated for 100k mi. and can often fail prematurely).
(Since you didn't post the MY, but list changing the fuel filter, I assume that you have a pre-'00 Boxster w/ Motronic 5.2, as the fuel filter isn't a maintenance item on the later cars)
See if the codes you get are any of these:
P0134, P0138, P0139, P0159, P0140, P0150, P0151, P0152, P0154, P0156, P0157, P0158, P0160, P1102, P1107, P1105, P1110, P1115, P1119, P1117,
P1121, P1124, P1126, P1123, P1125, P1127, P1129, P1128, or P1130.
These are all the p-codes relating to O2 sensors.
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