That's a pickle, a hole in a roof can cause all sorts of issues. The original repair could have missed something. You may have to remove the lining - not to hard in a wagon and get inside while someone gives it the hose test. Before that though, check the rubber concertina Hatch grommets for stress cracks.
good luck
R36 Wagon MY2010.5: Biscay Blue| Dynaudio and Nav| RVC| VW tow bar|
Mod highlights: ECU and DSG Tune| 3AA CCM and 7N0 Gateway| 3D colour MFD| MIB2 retrofit and 7N0 RVC| Quad LED tail, brake and indicator rings| Zimmermann Sportbrake rotors, composite pads| TPMS High| 2Q0 Blind Spot and RCTA| B8 rearview mirror|
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