Discrete throttle not responding

[vale.maio2]

KSP: 1.2.2 Windows 64 bit, Steam version

Computer: Windows 8.1 64 bit, Intel i7 4710HQ, 16 GB DDR3 RAM, GPU nVidia GeForce GTX 970M 3 GB GDDR5

Problem: I'm flying two separate unmanned vessels, both being controlled by a CH-J3 fly by wire controller; one is going to Eve, the other one is going to Jol. I can't control the throttle on both crafts discretely (which means with the Left Shift - Left CTRL keys); I'm able to change the thrust by either full on or full off (with Z and X keys). The problem exist with this save file only: opening my old saved game, the crafts throttle seem to work just fine. Here's what I've tried so far:

• Opening another save file: it works, I have issues with just my current save file.
• Remapping the keys for discrete thrust: didn't work on the current save, the new key binding works on the old save (which, again, had no problems from the start).
• Running KSP as administrator: didn't work.
• Removing all mods except MechJeb: didn't work.
• De-activating Windows 8.1 accessibility options (I'm not sure how it's called in English): they were never activated in the first place.
• Cussing at the keyboard: didn't work, but I felt slightly better.

I've read on the Interwebz that other people had the same problem with Shift and CTRL, and it was due to a program called Synergy, but I don't have such program installed on my PC (unless it's a buitl-in Windows feature).
I am also unable to revert any of the flights to the launch pad, as I improperly closed the game (read: ragequit). 

I have to point out the fact that I'm using the in-game cheats for infinite propellant and infinite battery power; don't judge me, I like to focus on the orbital mechanics rather than the rocket structure itself.

Mods installed:

MechJeb 2.6.0

Reproduction steps:

I have no idea, I can't reproduce it myself, if not with the save file in question.

Log:

[snip] I hope it's the right file, if not please let me know.

Thank you.

Edited January 15, 2017 by Vanamonde
Removed possibly compromised link.

[Vanamonde]

We had to remove your log file because it was setting off warnings, vale.maio2. We suggest you scan your PC for viruses.

That save may not be recoverable.  

[vale.maio2]

Virus warning on a .txt file? Sounds odd, but I'll take your advice and do a full PC scan. Sorry about that.

As per the issue I was having, there was no issue at all. I just had no comm signal to Kerbin, and since I hadn't being playing since a few months, I didn't know that you need comm to fly an automated rocket.

Thank you anyway.

EDIT: Chrome gives me a warning if I try to download the log file I uploaded yesterday, but I scanned it with Avast and it found no viruses. Really odd.

Edited January 15, 2017 by vale.maio2
added info