Check it is actually the correct driveshaft that is fitted.
Only time I've come across this before, it turned out to be a driveshaft for a different spec of the same car, which was about 10mm shorter but otherwise looked the same. Easily done if parts have been sourced from a breakers in the past.
Lowering is essentially just permently compressing the suspension a bit, unless you go beyond the design limits of suspension travel, the driveshafts should stay in place, just as if you hit a big bump and bottomed the suspension.