Check the vacuum solenoid inside the ink station and make sure the solenoid is opening and closing properly and when open allowing full air pressure (60 to 90 psi) through to the vacuum generator attached to the back of the extension tube by the quick disconnect. Check if the solenoid is leaking air also.
Check the 3/8” air line that runs through the tube jacket and attaches to the vacuum generator to make sue full air pressure is getting to the generator. It could be pinched off along the run somewhere.
Make sure the mill supplied air has not been turned down.
If the 5/8”drain line connected to the vacuum generator has never been cleaned out or if it has been lengthened and has high and low spots where dye can accumulate and build up this can cause back pressure. It has to be well vented with no restrictions.
The vacuum generator can be taken apart and cleaned. If it is dirty or has sucked a piece of paper into it, this can weaken the vacuum.
If the drain line is submerged in dye in a tank can cause this also.
The system is ~ 3 or so years old and if the vacuum system has never been flushed out that may be all it needs.
Have there been any changes to the system or environment around the system?