The vast majority of bugs I have reported have been confirmed by other users, two of which you confirmed for me, too.
 
Let's wait for these plugins to see wider usage before jumping to conclusions.

I hate to say it but your interface is not helping you. I had the same model and it's a USB 1.1 design. I had no end of weird and random glitches until I dumped it and bought something modern. The Roland drivers were not good on that device. I know you will say it's only Sonar where you have trouble, and it was the same for me. As illogical as it sounds, life got better once the Cakewalk interface was replaced.

The problem is repeatable on my PreSonus AudioBox 22VSL, Tascam US-1641, US-1800 and US-16x08.
 
Of all of these, my Cakewalk UA-25EX has given me the least trouble.
The drivers have been updated regularly by Roland.

I should probably take advantage of the sig feature on this forum, save unnecessary repetition.
 
I'll include links to the bugs and incorrect documentation and the threads in which users confirm and help me build a recipe.
 

Which audio settings do you have, I mean 44.1/48/96, 16/24, ASIO buffer size?
Which settings under LP "Expert" options do you use?
 
I have tried with several combinations, but everything works like excepted. But may be other use different from your options.

It could be a virus your virus software missed.  This happened to me, and I went to http://www.eset.com/us/on...nner/?CMP=knc-Google-G|S-US-BR-C-Other|B&gclid=COK-nKbbucwCFcRgfgodAm0Gvg They have a free online scanner and they found and fixed my problem.  I had 3 different virus' on my computer that were all missed by Windows Defender and Hitman Pro.  This online scanner found them and removed them for free.  The scan took several hours on my internet connection to complete, but it was well worth the effort.  Maybe something you want to check out.

In my case the Stop button on the Transport greys out and the song just keeps playing.

It is not related to effects in my case. This happens even on songs I have zero effects added into the song file.

It does happen after I've been playing / recording a soft synth. Any soft synth, not a particular one.

Seems to happen at random.

Happens frequently for me. I'm living with it, still happy with Sonar. But this is a nuisance.

I'm very glad I'm seeing others experiencing this as well. I've had this issue since several releases of Platinum. Not sure when it started, but for at least 4 months now.

Just for additional reference: I did as OP instructed in orig post. I added the new LP eq to master bus-no issues. I then added the new LP MB-no issue. I then added Isotope 5 to the master bus-all three active in master bus and still-no issues. I just used various presets from all 3 plugs. Am I doing something wrong to try and reproduce this. Because everything is fine. Tried with recorded audio-just silence, Then tried with recorded guitar track noodling. Still no issues. 
I am on latest SP update. 
Edit: Should mention both the spacebar stop/start and the stop button work as they should-and no stutters. 

I'm experiencing similar symptoms to the OP, but not from doing the same actions.   It's happening to me in files that have absolutely no effects in them.  I recognize it's probably just me and specific to my computer.  But it's interesting to see the symptom is happening to others.
 
For me, unlike the OP, once the Stop button on the transport is greyed out there's no way to get the Stop button active again.  I am able to save the file.  I use Control Alt Delete - Task Manager to get out of Sonar.  I can then open the file again and all is well.
 
It's very peculiar.  I'll stop mentioning it now, unless I see it happen to someone else again.  I've noted this before, but it seems to not be happening to the general population (one would think it would never happen, so I'm guessing it's something related to my machine).

bz2838
It could be a virus your virus software missed.  This happened to me, and I went to http://www.eset.com/us/on...nner/?CMP=knc-Google-G|S-US-BR-C-Other|B&gclid=COK-nKbbucwCFcRgfgodAm0Gvg They have a free online scanner and they found and fixed my problem.  I had 3 different virus' on my computer that were all missed by Windows Defender and Hitman Pro.  This online scanner found them and removed them for free.  The scan took several hours on my internet connection to complete, but it was well worth the effort.  Maybe something you want to check out.

I was searching for a solution to another issue (freezing while looping) when I ran across this post. I downloaded Eset's trial and it found sixteen instances of malware on my machine that my religiously used Windows Defender did not find. And removing those little buggers fixed my lock up issues with Sonar. Sixteen! Holy moses.
 
OP, bz2838 gives good advice. Have you tried scanning for malware with a good security tool?