Ultimaker 3 extruding problem when using support material

[Benighted 0]

Hi,

 

I'm having a strange problem when I use any support material in printcore 2 while printing with my Ultimaker 3 Extended. After 50'ish layers the printcore 1 starts having problems to extrude the material while the printcore 2 prints flawlessly. After about 50 layers the problem disappears and the printcore 1 start extruding correctly and the rest of the print is as it should be. This happens every time when using the support material and it always behave about the same way. Few good layers, then the Printcore 1 stop extruding well for a while and after that the rest of the print is good. 

 

I've cleaned the printcores and used different materials and different material feeding racks so that the material shouldn't get stuck anywhere. This problem also occurs only when I use the printcore 2 for support printing which indicates something else than a clog in a printcore, stucking material feed or faulty z-axle movement. This problem also doesn't occur when I use the printcore 1 for support printing so it's not about the printing support per se.

 

Here's a picture from a failed print if it helps anything. The printer is almost 2 years old and the problem appeared about a month ago.

 

Thanks in advance!