When using /server -n <server address> <port> to open a tab for a server, it will forget the specified port when connecting to the server using the connect button.
/server -m <server address> <port> works fine.

Also, when doing /list, channels which have 2 or more hashes (#) at the beginning of it don't appear.

Both of these bugs were tested and confirmed on mIRC 7.36, and the 2nd bug was also confirmed on mIRC 6.35. I didn't test the 1st bug on 6.35, but it could be there.

The second is expected behavior as a result of the "hide non-text channels" under tools > channel list. I believe this behavior is changing in the next release to display channels with doubled prefixes.

Thanks for your bug report. Both of the issues you describe seem to be expected behaviour.

The first issue: when you connect to a server, mIRC will always cycle through the ports listed for that server or network in your servers list. If you have an entry in your servers list for that server or network, and you want the server to always use a specific port, you will need to edit the ports setting for that entry.

The second issue: as mentioned in the above post, is controlled by the "hide" option in the channels list window. However, mIRC will be adding an exception to this feature for double prefixes. You can test this change, and other changes, in the latest beta.

If that is the case with the 1st issue, could there be a way of prioritising the servers in the server list in a future version of mIRC, so it would connect to the first server first, which could be using +6697, then the next server in the list, or an option to connect to the same server every time?

mIRC will connect to servers in the order that they are listed in the servers list. As the servers list is sorted alphabetically, you can change the server description for each server so that it is sorted in the order that you want, for example by prefixing each server description with a number. Note that "random" servers are always sorted to the top of the list for a network.

If you want to connect to the same server every time, you can either create a new group with just that server and connect to that group using /server group. Or you can delete all other servers in that group, so that mIRC will only connect to that server. This is because mIRC searches through your entire servers list to find matching groups/servers when determining which server to connect to next.