I think I have same issue here on RBD52G-5HacD2HnD with RouterOS v6.45.6
I have two subnets:
192.168.1.0/24 is for ordinary home router usage. Router itself has address 192.168.1.1 and the rest address space is used for DHCP pool for connected devices.
192.168.2.0/24 is DHCP pool for devices connected to the L2TP server configured on the router.
When I was setting-up NordVPN tunnel (using manual on Mikrotik's wiki page) I decided to route only 192.168.2.0/24 to it so I won't disturb ordinary internet connection at home while doing so. Also I was adding to exceptions some destination addresses which won't go through the tunnel and will be routed directly.
Now after I have configured all that I also want 192.168.1.0/24 to be routed through the NordVPN tunnel so I add it to the corresponding address list. And after that I get a strange situation:
On 192.168.1.0/24 I got above-mentioned problem where I got 25Mbps download speed (maximum for my ISP connection) and nearly 0Mbps (about 0.02Mbps) for upload speed. So browsing on the Web lags a lot. But connections in the exceptions list are going fine at full speed.
At the same time on the same machine when I connect to the VPN server on the router and accordingly get to the 192.168.2.0/24 subnet everything works perfectly and I get maximum download and upload speeds permitted by my ISP through the NordVPN tunnel.
Any ideas how to fix this upload speed problem?
I am really a newbie in all this, so firstly in my case it can simply be some stupid mistake in config and secondly please speak simplier in answers
------- UPDATE -------------
I have disabled fasttracking as described by sindy. It helped but didn't solve the problem. With fasttracking disabled I have about 4Mbps upload speed.