Welcome to the Forum
Maybe you need to Complete a PX1 Clean Up.
https://forums.evga.com/FindPost/2947719 & https://forums.evga.com/FindPost/2947737

Latharion
I am encountering the same issue as the OP.  I followed the procedures suggested by bcacvnaugh but the results were the same.  The PrecisionX1 ver 1.0.4.8.0 does not properly implement the "Start With OS" setting, at least on some systems.  It does properly implement the "Start Minimized" setting.  This is happening in both Windows 7 and Windows 10.
 
To be clear, I tried this multiple times.  I followed the "clean PrecisionX1" procedures outlined above, using the following order...
 
Uninstall Precision X1 >  use the "clean PrecisionX1" procedure > reboot > install Precision X1 (ver. 1.0.4.8.0) > ensure that the "Start with OS" setting is marked as "on" > reboot.
 
This seems to be a simple programming bug.  It is annoying and I hope someone from EVGA reads this and informs the programmers.

Is apply Previous setting on Reboot also checked ?

@Cool GTX  No.  "Apply Previous settings settings on lodad" is not selected (and never was). 
 
@bdary I never mentioned "Apply previous settings on load", and that particular setting was never selected.  Also, I did click "Apply" after selecting "Start with OS". 
 
In order to maintain a reliable boot environment, I always have PrecisionX1 start in it's default config, then I select the profile I want (usually "0"), click "Load" then "Apply"

I am having this issue right now as well.  Found this thread as I was trying to solve it.
 
Edit:  Ahaha, the rig in my signature on this forum, wow, that is old.  Rocking a GTX 460 back then, hehe.

ElliottSmith
I am having this issue right now as well.  Found this thread as I was trying to solve it.
 
Edit:  Ahaha, the rig in my signature on this forum, wow, that is old.  Rocking a GTX 460 back then, hehe.

Maybe you need to Complete a PX1 Clean Up for you Non-GTX 460 Graphics Card
https://forums.evga.com/FindPost/2947719 & https://forums.evga.com/FindPost/2947737
 

Unfortunately none of those steps work.  I have not had an issue with the program running at startup until I updated.  I have since done all the troubleshooting to no avail.

Just wanted to chime in that this issue also affected me after the 0.4.4.0 update and was not resolved with the subsequent update.  Precision X1 will not automatically start on system startup, despite that setting being selected in the options.  I have done the usual "change settings, close Precision X1 to ensure they're saved" dance, and the settings are definitely saved/set, but it just doesn't start on startup like it used to.  I can start it manually and everything mostly works fine from there (aside from Precision X1 almost always hanging/locking up after running for long periods of time, which has always been the case for me).
 
This is the standalone version of Precision X1.
 
PC specs as follows:
Intel Core i7 2600k, ASRock Fatal1ty P67 Professional MB
16GB RAM
eVGA RTX 2080Ti Black Edition
Windows 7 Ultimate, fully up-to-date

One further note on this issue (which is still happening as of the latest 1.0.0.0 version)...
 
I tried simply putting a shortcut to Precision X1 into my startup folder, but it still refuses to start on boot-up.  So this might indicate that where things are going wrong in PX1 deals with something in its startup/initialization (and perhaps some prerequisite on the OS not being ready at startup), rather than the "Start with OS" setting not being applied properly.

Asryan
I had to remove 1903 update to make it work normally again

Thanks for Sharing your "fix"

Asryan
I had to remove 1903 update to make it work normally again

Glad that worked for you.  I am still on Windows 7 (but not for long), and this issue specifically coincided with the 0.4.4.0 PX1 release (i.e.; it was not tied to a Windows update).

Please do the following:
 
Download and install the latest version of Precision X1
 
Press "Windows Key + R"
 
Type "shell:startup"
 
Press enter
 
Drag your Precision X1 shortcut into the folder that pops up
 
Right click the new icon and hit "Properties"
 
Select the "Compatibility" tab
 
Check "Run this program as Administrator"
 
Close all windows
 
Reboot
 
 
 
The problem is caused by lack of elevation and these steps should fix it
 
Hope this helps
 
 
Regards,
 
antiPLUR

Just a quick update; after doing my (in-place) upgrade from Windows 7 Ultimate to Windows 10 Pro, this issue seems to be resolved for me.  I can't say for sure if a Precision X1 update may have fixed it previous to now, as I had the "Start with OS" turned off since it had stopped working (see my post above), but at present this is functioning properly.