First thing to look at is temperature. My default Felix Ninjaflex profile in cura is at 200C 95% flow and bed at 40C. I have not printed flexible filament yet and I don’t know if 200C is hot enough for ninjaflex (they say 210 is minimum range).
Second thing to check is the grip! What drive gear/wheel do you have on your extruder motor? The new grooved one 35 should be better at guiding the filament into the hot-end, but you should take care to align it too (groove aligned with hot-end input hole)! Also check your extruder tension spring because a high tension and grip is important especially for flexible filament.
Third thing is the nozzle opening. If you are not extruding a fine line your nozzle might be semi clogged. It might be because of the material you printed previously. Heat up your hot-end to 240C and use the 0.35 mm dremel drill bit to clean your nozzle carefully. Then check the extrusion again. A side note for this. The z bed leveling calibration is also important! If the first layer is really squished then you might experience filament grinding, nozzle semi clogging and build up. If you are printing at 200 microns you want the first layer to be no less than 180 microns. Squished first layers stick to the bed surface better, but can create other side effects that might cause the problems you are having.
One more thing is print speed. Flexible filament should be printed max 20mm/s, unless you know your printer can print it faster. Cura has the lowest default setting at 30mm/s, you should change that to 20mm/s and if it still fails lower it more. A side note for this is the extruder steps per mm calibration. Calibrate it with PLA first and then test and calibrate the flow for ninjaflex. Extruder steps if not calibrated affect the print speed. If you want to extrude 10mm of flexible filament but you actually extrude 12.7mm or 8.2mm, then your speed and dimensions will not be accurate and will create problems.
There is a good video guide 27 that explains things you should know when printing flexible filament.
If none of the above tips helped you, I am sure if you e-mail felix printers support, they will help you out. Suggest tests to do and step by step configure your printer. They have responded to my support tickets every time in 1 or 2 days!
First of all check the temperature and grip. You need to watch the print speed I recommend 15 mm/s. You can look at a clogged nozzle by putting PLA or ABS in the print head and then try to see if it comes out semi curved or to the side. It should come straight down.
I put my money on underextrusion caused by bad filament grip. The Felix 3.0 has one big weakness: the drive gear is really bad and starts slipping as soon as there is a bit too much friction (either in the nozzle or in the feed line). I even had this problem with regular PLA. I solved it by installing a new drive gear with curved grooves (or you can upgrade to Felix 3.1).