That's because you are doing it wrong! 
Don't route DNS Traffic from VLAN to VLAN but instead add some VLAN Interfaces to your Pi-Hole Server so it has a simple local connection with every Client in each VLAN
If you want I can write up a Tutorial for this in English ?
In case you speak Dutch or feel like using Google Translate then click here : https://gathering.tweakers.net/forum/list_message/57865570#57865570