Do you have the marker enabled in the mIRC Options/Display/Options marker dialog? If you do, you should not have to press Control+L to turn it on in a window - it will display automatically when it needs to.
Control+L will not change the position of the marker. It will only show the marker where it was the last time you made that channel window active. If you manually turn off the marker with Control+L, it will no longer be displayed in that window until you manually turn it on again.
Regarding the marker position, unfortunately I still have not been able to reproduce an issue here. I joined several channels and monitored them for an hour or so, returning every so often to check the marker position. The marker changed position as expected to mark the last time I made that channel window active.
