Can't access hosts via certain ports from a computer connected to an hEX-S

Recommend one bridge and use the vlans to separate out separation of subnets.
As for groupings the better ways to accomplish this and also support firewall rules are
interface lists and address group lists.

Rule of thumb if you have whole as single subnet or part subnet use IP addresses
If you have a a group of interfaces use interface list.
If you have one or more specific IP addresses use IP Addresses.

Obviously since one can put subnets into address lists there is lots of flexibility but I tend to keep address lists to when I have individual IPs in the mix.

Just a heads up the best ref for vlans is
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1

I will look at your config soon, just need to go shopping first…not sure i agree with the poster above me, i wouldnt jump on it yet.
Change your config to a single bridge and read the ref first.