Upon placing a docking port against another docking port where both are set as passable the second port is not connecting the living space together, anything attached above it is not included. However, removing the second port and re-attaching it resolves the issue and anything attached above it now works OK.

Closing due to inactivity.

I believe since much refactoring has occurred, this problem should have been resolved. If I do not hear anything within a week. I will close.

Are you sure that you are using the latest version? This was the way it worked in 1.0.5.0 and below (ie you had to decouple, and then dock) buy in 1.0.6.0 a change was made to that coupled (rather than just docked) docking ports would be passable.
If you are on the latest version, then could you provide a screenshot or similar to illustrate the problem.
Thanks for taking the time to log this issue.

Isolating the situation in a test install (clean game, no other mods, fresh dsave) using a fresh 1.0.6.0 install, ModuleManager 2.1.5, Toolbar, The BobCat MIR parts, and my MM config I was using.

The config in question is written like this:

//ISS Common Berthing Module
// From ISS Community

@PART["ISS?CBM?dockport"]:HAS[!MODULE[ModuleConnectedLivingSpace]]
{
    MODULE
    {
        name = ModuleConnectedLivingSpace
        passable = true
    }
}


//ISS APAS 69 Port
//From Soviet Pack (CONFUSINGLY!!)
@PART[APASport]:HAS[!MODULE[ModuleConnectedLivingSpace]]
{
    MODULE
    {
        name = ModuleConnectedLivingSpace
        passable = true
    }
}


//MIR Docking Ports (Probe and Drogue types)
//From Soviet Pack
@PART[Mir_DockingPort*]:HAS[!MODULE[ModuleConnectedLivingSpace]]
{
    MODULE
    {
        name = ModuleConnectedLivingSpace
        passable = true
    }
}


// This stops the Cover Cap from allowing passage as it's, well, supposed to be a cover!
@PART[Mir_DockingPortCoverCap]:HAS[!MODULE[ModuleConnectedLivingSpace]]
{
    MODULE
    {
        name = ModuleConnectedLivingSpace
        passable = false
    }
}

I can confirm that in this enviroment it is still happening, Screenshots attached,

OK, I have looked into it and I can replicate the problem you are seeing.
I can also replicate the situation using stock docking ports, so we can conclude that there is nothing wrong with either the bobcat parts or your .cfg file. There are a few more subtleties:

1. if you remove the second docking port and re-add it then it does get included in the CLS space.
2. at this point other docking ports can be used to replace the second docking port, and that will be included in the CLS space. This is the case until the first docking port is removed and a new one used.
3. If you just add another pod to the top of the second docking port then they will all get included in the same space.

So I am not entirely sure what is going on - something in CLS's algorithm, but it can be easily worked around, and you can be assured that your .cfg file is correct.

Do you have plans to ship for CLS config with the bobcat pack or make it available to ship with CLS?

I am sure I found when attaching a docking port above the first time anything above it didn't get included in the CLS space. Only after I removed and reattached the port did it the ninclude stuff addes above in the CLS space. Sorry, should have tested that!!

EDIT: Yeah, sorry. Tested and you are correct, it resolves as soon as you attach anything CLS enabled above the port, can confirm from here.

Adding a port, adding another above it, removing it and throwing it away then adding a fresh docking port of the same type does not get included in CLS Space. Whatever is going on is dependant on the individual part added, not the general situation.