Aero Snap hotkeys not working after reboot my computer.
I have Explorer Integration enabled, unassigned Win + Left and Win + Right in ConEmu.
Aero Snap hotkeys works again after I opened the ConEmu Settings window.
If you disable hotkeys in ConEmu (what exact actions?), than Aero Snap is done by Windows, and ConEmu can't handle it at all.
I have this showing in "Key & Macro"
[Disabled] Decrease window width (check ‘Resize with arrows’)
Aero Snap hotkeys not work after boot, but it works after I opened the "ConEmu Settings".
I changed other hotkey assigns "Snap ConEmu window to the monitor's left edge: WindowMode(6)" and reboot my computer, Aero Snap hotkeys works as expected, and no need to open "ConEmu Settings".
If you disable hotkeys in ConEmu (what exact actions?), than Aero Snap is done by Windows, and ConEmu can't handle it at all.
Is there any hope for letting windows take care of it? Would it fixing the positioning bug?

bump. I feel like this is quite an annoying bug.
For me Aero-snap started working again simply by left clicking on the ConEmu icon in the system tray. I didn't open conemu settings or anything else. Solution found by way of Andre Neves (http://superuser.com/a/1091991/16966), who reported the issue with ConEmu 160619 [64]. I'm using 160612 [32], and here's my keyboard settings:

[Disabled] Decrease window width (check ‘Resize with arrows’)
These hotkeys are not related to "snap" at all. They tries to do exactly what is described: increase/decrease the window size (by one cell actually).
I don't understand your problem. Is it still actual?
I'm not sure about the 'resize with arrows' part you quoted Maximus, but for me I have to click ConEmu systray icon every time I logon to Windows in order to regain Aero Snap hotkeys.
Also, on this 1st systray click, when ConEmu opens but there is no command prompt. I close the window, Aero Snap works. I run ConEmu again (from start menu, because systray icon is gone), command prompt is available, and Aero Snap still works.

Something strange here. In the screenshot from systray-click that I just uploaded ConEmu is v160612 [32], but the entry in Control Panel >> Add/Remove Programs is 161206x64.

...Running ConEmu from Start Menu is the newer x64. Running ConEmu by "Start >> Command Prompt" shows the older 32bit ConEmu. So I have it installed twice somehow.
From newer x64 ConEmu under _Settings>> Integration>> Default term_ I set "Force ConEmu as default terminal for console applications" and 'Register with OS on startup". Now after a fresh login Aero Snap works and opening Command Prompt shows x64 ConEmu shell. There is no systray icon anymore but that's okay because I didn't really use it anyway.

@maphew Installer updates only files installed by it (msi). I have no idea how did you obtained old 32bit exe.
http://conemu.github.io/en/Installation.html#installer
Anyway, bugs from obsolete versions have no value cause they meaty be fixed already.
It happened to me today that win + (shift) + arrow shortcuts suddenly stopped working. I have found this answer on SuperUser and it really fixed the issue.
The first click on the systray icon (to minimize ConEmu) didn't help, but after clicking it once more (to restore ConEmu), win + (shift) + arrow shortcuts started to work again.
I didn't do any changes to ConEmu recently (upgrade, configuration, etc.).
I'm using ConEmu version 170517 (x64) on Windows 7 x64.
Most helpful comment
For me Aero-snap started working again simply by left clicking on the ConEmu icon in the system tray. I didn't open conemu settings or anything else. Solution found by way of Andre Neves (http://superuser.com/a/1091991/16966), who reported the issue with
ConEmu 160619 [64]. I'm using160612 [32], and here's my keyboard settings: