On a 2001 model the vacuum hose for the fuel pressure regulator should go directly from the rubber boot on the intake cross-tube to the regulator on the fuel rail.
It sounds like you may have the vacuum lines on incorrectly. The diagram above is for a 2001 2.7L manual. There is more discussion of it here: https://986forum.com/forums/boxster-general-discussions/64576-vacuum-line-clarification.html#post518618
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