Just a wild stab here, but in trying to reproduce the problem, have any of your attempts been made with a system that does not require a login screen at startup? I am configured to boot directly into Windows, with no logon screen (and so no password required).
As for going back to 3.6.8, I was going to consider doing that if the problem persisted, but I preferred not to lose the latest functionality. I will note that I don't recall having this problem until 3 or 4 months ago, which would seem consistent with the issue occurring only with the new upgrade. Then again, if I *had* been "losing" some startup tray icons with the old version, but it was infrequent or mostly affected infrequently-used icons, I might not haven taken notice.
Also: After posting, I noticed that -- while a couple tray icons that were going missing almost 100% of the time were now *showing up* 100% of the time after my fix (including one that I was most concerned about) -- there were still occasionally some missing ones, though a lot fewer and a lot less frequently than before. So, while still keeping the ""start automatically for this user" option UNticked, I tried moving the startup shortcut I created for Classic Shell from C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup to C:\Users\<Username>\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup. (The five other Startup shortcuts I have remain in the All Users startup.) In the three days since making that change, I have had 100% of the tray icons appear about 90% of the time, i.e., a nearly-complete fix (I did quite a few reboots to check.)
One more thing: Back when I still had auto-start checked and tray icons were often going missing, I tried using System File Checker. It found roughly five files with integrity violations and repaired them. Then during the next two boots all my tray icons showed up. But then some started going missing again, so I reran sfc, it found and repaired the same files, and the tray came icons back 100% for another few boots. And the pattern kept repeating. But since unticking the auto-start option, sfc has come up clean every time. While these files don't mean anything to me, here is a portion of the log that shows files that kept appearing as corrupt when auto-start was ticked:
2014-08-25 00:05:31, Info CSI 00000324 [SR] Beginning Verify and Repair transaction 2014-08-25 00:05:32, Info CSI 00000325 [SR] Repairing corrupted file [ml:76{38},l:74{37}]"\??\C:\Windows\SysWOW64\wdi\perftrack"\[l:24{12}]"authui.ptxml" from store 2014-08-25 00:05:32, Info CSI 00000326 [SR] Repairing corrupted file [ml:520{260},l:74{37}]"\??\C:\Windows\System32\wdi\perftrack"\[l:24{12}]"authui.ptxml" from store 2014-08-25 00:05:32, Info CSI 00000327 [SR] Repairing corrupted file [ml:520{260},l:76{38}]"\??\C:\Program Files\Internet Explorer"\[l:34{17}]"ie9props.propdesc" from store 2014-08-25 00:05:32, Info CSI 00000328 [SR] Repairing corrupted file [ml:76{38},l:74{37}]"\??\C:\Windows\SysWOW64\wdi\perftrack"\[l:38{19}]"wow64_ieframe.ptxml" from store 2014-08-25 00:05:32, Info CSI 00000329 [SR] Repairing corrupted file [ml:520{260},l:74{37}]"\??\C:\Windows\System32\wdi\perftrack"\[l:28{14}]"LDDMCore.ptxml" from store 2014-08-25 00:05:32, Info CSI 0000032a [SR] Repairing corrupted file [ml:520{260},l:76{38}]"\??\C:\Program Files\Internet Explorer"\[l:30{15}]"pdmproxy100.dll" from store 2014-08-25 00:05:32, Info CSI 0000032c [SR] Repair complete 2014-08-25 00:05:32, Info CSI 0000032d [SR] Committing transaction 2014-08-25 00:05:32, Info CSI 0000032e [SR] Cannot commit interactively, there are boot critical components being repaired 2014-08-25 00:05:32, Info CSI 0000032f [SR] Repairing 6 components 2014-08-25 00:05:32, Info CSI 00000330 [SR] Beginning Verify and Repair transaction 2014-08-25 00:05:32, Info CSI 00000331 [SR] Repairing corrupted file [ml:76{38},l:74{37}]"\??\C:\Windows\SysWOW64\wdi\perftrack"\[l:24{12}]"authui.ptxml" from store 2014-08-25 00:05:33, Info CSI 00000332 [SR] Repairing corrupted file [ml:520{260},l:74{37}]"\??\C:\Windows\System32\wdi\perftrack"\[l:24{12}]"authui.ptxml" from store 2014-08-25 00:05:33, Info CSI 00000333 [SR] Repairing corrupted file [ml:520{260},l:76{38}]"\??\C:\Program Files\Internet Explorer"\[l:34{17}]"ie9props.propdesc" from store 2014-08-25 00:05:33, Info CSI 00000334 [SR] Repairing corrupted file [ml:76{38},l:74{37}]"\??\C:\Windows\SysWOW64\wdi\perftrack"\[l:38{19}]"wow64_ieframe.ptxml" from store 2014-08-25 00:05:33, Info CSI 00000335 [SR] Repairing corrupted file [ml:520{260},l:74{37}]"\??\C:\Windows\System32\wdi\perftrack"\[l:28{14}]"LDDMCore.ptxml" from store 2014-08-25 00:05:33, Info CSI 00000336 [SR] Repairing corrupted file [ml:520{260},l:76{38}]"\??\C:\Program Files\Internet Explorer"\[l:30{15}]"pdmproxy100.dll" from store 2014-08-25 00:05:33, Info CSI 00000338 [SR] Repair complete
I don't know if there's any significance to this, but I have IE10 even though I see a filename above called ie9props.propdesc.
I have also attached the whole sfc log from back when I had the Classic Start Menu auto-start option ticked.
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