Tried TM 4.5.5633 stable and 4.5.5648beta in FF 57.0.1 x64 in win10.

The issue I have is this:

• (initially TM works ok)
• I close and restart FF: in the restored pages (session restore), sometimes the scripts run in the page, but frequently other they don't. (although the counter in the toolbar button still displays each matching counter) . Let's suppose that they do work.
• I disable TM via its toolbar button menu(the 1st entry), reload the page(F5) to make sure the scripts are not working anymore, and then re-enable it via the toolbar button:
• no scripts are working anymore (although the counter in the toolbar button still displays each matching counter) .
• At that time, no matter how many times
  I either disable+re-enable TM the toolbar button,
  or I disable+re-enable TM via about:addons,
  they don't run in the page anymore.
• The only solution I've found is, when this happens,
  to close+re-open FF (at that time, the scripts will still not be working), and disable+re-enable TM via the toolbar button. <-- but even this, it doesn't fix the problem every time, I may have to disable+re-enable TM multiple times and/or restart FF in order to fix this .
  And, If I try to disable it then, the issue re-occurs (almost) every single time.

I haven't managed to recreate this with a fresh FF profile.

Here is a log from Browser Console (TM 4.5.5633 stable)
as I disable TM via the toolbar button (having only TM enabled):

Try to load layout default  layout.js:3
No matching message handler for the given recipient. MessageChannel.jsm:703
Storage: use chromeStorage  storage.js:19
Unchecked lastError value: Error: Could not establish connection. Receiving end does not exist. ExtensionCommon.jsm:407
Storage: test -> start  storage.js:11
Storage: test -> set after 502ms  storage.js:11
Storage: test -> get after 504ms  storage.js:11
Storage: test -> remove after 1010ms  storage.js:12
Unchecked lastError value: Error: Promised response from onMessage listener at addListener@moz-extension://eacdd3d4-ef20-4256-ae58-3eb85f85fa83/rea/common.js:3:291 went out of scope ExtensionCommon.jsm:407

and, as I re-enable TM via the toolbar button:

Try to load layout default  layout.js:3
Unchecked lastError value: Error: Promised response from onMessage listener at addListener@moz-extension://eacdd3d4-ef20-4256-ae58-3eb85f85fa83/rea/common.js:3:291 went out of scope  ExtensionCommon.jsm:407
Ignoring response to aborted listener for 575-4
Ignoring response to aborted listener for 576-4
Ignoring response to aborted listener for 577-4
Ignoring response to aborted listener for 578-4
Ignoring response to aborted listener for 579-4
Unchecked lastError value: Error: Could not establish connection. Receiving end does not exist.  ExtensionCommon.jsm:407
Storage: use chromeStorage  storage.js:19
Storage: test -> start  storage.js:11
Storage: test -> set after 502ms  storage.js:11
Storage: test -> get after 503ms  storage.js:11
Storage: test -> remove after 1005ms  storage.js:12

I don't have any special TM settings enabled
(especially, in Settings | General, the "Auto reload pages" setting remains disabled, as by default)

If there's anything more I can provide to help, please ask.

I have ~200 userscripts installed.
For reference, with the same number of scripts in Greasemonkey 4.0 or 4.1beta6
I didn't have such an issue.

My other addons are uBlock Origin 1.14.20, Reddit Enhancement Suite 5.9.3beta and Stylus, but even if I disable them, the issue still occurs.