I haven't been starting second copies manually.
Originally, I was running it the default way (FAH runs at startup). Then, based on PantherX's comments, I decided to uninstall and try installing it without the auto-startup feature. So now, I run it (once) manually to start it. Either way, it didn't make any difference, since I was getting the same sorts of problems in both scenarios.
I know I can pause processing through web control or advanced control. The problem is that sometimes FAH shits itself and stops being able to control its processes. I pause it, but FAH continues to take up 99% of my GPU and/or CPU. Or, I set it to "idle", and the FAH icon gets zzz's on it, yet it continues to fold furiously even while I'm using the computer (this last problem is referenced in the original thread title).
Look, I think if we're going to solve this, we need to look past basic user error. I'm prepared to accept that it may be PEBKAC, but only of some more complicated and/or leftfield variety. I think the basic stuff has been covered already. I've tried all the suggestions you guys have given me, but the problems keep recurring. So, I don't think it's something basic like bandwidth problems, firewall settings, or me using the software the incorrect way. I think it's more likely to be some sort of hardware or software conflict, bug, or else I've gone and screwed something up in some creative way.
The thread is long now, so I'll reiterate my problems here:
-Folding usually works fine
-But some WUs fail to receive a completion acknowledgement. That is, they complete, they upload, I get points, but they still say "sending" on my FAHcontrol, and never go away. After they get to about "upload 99%" there is no more trace of them in the logs
-Eventually, these 'unsent' WUs pile up.
-Eventually (not sure if this is related to previous problem or not), FAH starts becoming less reponsive
-Sometimes FAHcontrol is inaccessible (web control times out, advanced control greys out) even though folding itself continues
-Sometimes FAHcontrol loses the ability to properly control the cores: pausing it doesn't pause them, they continue folding even when I set it to "idle", and the uninstaller isn't able to successfully close them down
-It seems that after about a couple of weeks, these problems start occurring, and get progressively worse
-After a clean install, the same pattern restarts: works fine, then slowly the above problems start coming. I've done about a dozen clean installs this year, using various different settings (default, custom, autostart, manual, beta, normal), with no difference.
-In the past, I folded just fine with this PC (same windows installation, mostly the same hardware), and didn't have any of these problems. The only changes I can think of between now and then are a new PhysX card (GTX650ti), and a new netgear router. The router, and my internet in general, works fine in every other department (browsing, steam, streaming, downloads, home network, streaming PC games to nvidia Shield). I've also started running nvidia Experience since that time.
My system:
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07:44:41:******************************* System ********************************
07:44:41: CPU: Intel(R) Core(TM) i7-4770K CPU @ 3.50GHz
07:44:41: CPU ID: GenuineIntel Family 6 Model 60 Stepping 3
07:44:41: CPUs: 8
07:44:41: Memory: 15.93GiB
07:44:41: Free Memory: 12.68GiB
07:44:41: Threads: WINDOWS_THREADS
07:44:41: OS Version: 6.1
07:44:41: Has Battery: false
07:44:41: On Battery: false
07:44:41: UTC Offset: 10
07:44:41: PID: 8836
07:44:41: CWD: C:/Users/Dave/AppData/Roaming/FAHClient
07:44:41: OS: Windows 7 Home Premium
07:44:41: OS Arch: AMD64
07:44:41: GPUs: 3
07:44:41: GPU 0: NVIDIA:3 GK110 [GeForce GTX Titan]
07:44:41: GPU 1: NVIDIA:3 GK110 [GeForce GTX Titan]
07:44:41: GPU 2: NVIDIA:3 GK106 [GeForce GTX 650 Ti]
07:44:41: CUDA: 3.5
07:44:41: CUDA Driver: 6000
07:44:41:Win32 Service: false
Other points of note:
-I'm running Win7 64bit Home Edition
-I've seen very few folding errors in any of the logs I've looked at
-My CPU is overclocked. It's stable with overnight stress tests and regular usage, with temps well within the safe limits
-My motherboard is an Asrock Z87 Extreme9/ac. Overall it works fine, but it seems to have some minor problems with USB not always getting power at startup (sometimes can't enter BIOS because of this - have to reset PC couple of times until USB gets power).
-My Titans use a custom vbios by svl7 that removes nvidia's GPUBoost2.0 feature. In other words, it gives the Titans stable clocks rather than variable ones. I also have them mildly overclocked. They work without problems in heavy gaming, with safe temps.
-The Titans are set to SLI, and the 650ti is dedicated to PhysX