If you configure the native VLAN for the MX and MS to be 99, then any other VLAN will be tagged.
The switch defaults to using VLAN1 for its management VLAN. So it would have sent a packet with a tag of 1 on it, causing it to use VLAN1 on the MX, not VLAN99.
IMHO, the best solution is to leave the native VLAN as 1 on the ports between the MX and the MS.
Another solution is to configure the MS to use VLAN99 instead of VLAN1 for management.