When you look for Restore Points you should hope to see them like this with several Restore Points listed:
If you have no Restore Points I would consider that another problem that you should look into and there could be an explanation for that - but I would fix it if it needs fixing.
Do you know the name of this package tracking software you installed and are you able to describe how you cleared it off your computer... from Programs and Features (aka Add/Remove Programs) or something else? The software maker may have a certain way to uninstall/remove their stuff from your system.
Sometimes uninstalling things will leave behind unwanted startup items that can cause these popups when you restart since the software has been removed but the startup item has been left behind.
You can download from Microsoft Autoruns and use it to find the startup item, disable it, then when you are sure things are good you can delete the startup item entirely so your startup is not sloppy.
Read through this description and report back your findings:
It might be easy to get rid of the error message by doing something like disabling the startup item in msconfig (if you can even find it), but I suggest you fix the problem and not just fix the symptom of the problem by just eliminating the startup message.
I would also not recommend that you start poking around in the registry unless you have a backup since there is no "undo" or "quit without saving" option in regedit. If you make a mistake, that's it.
Those ideas offer "quick" and sometimes risky relief of the symptom, but may not actually fix the problem. I would also be wary of ideas that begin with the words "try". You do not need to try things, you need to do things.
Here are comprehensive instructions that will keep you safe and resolve your issue the "right" way.
Describe your current antivirus and anti malware situation: McAfee, Norton, Spybot, AVG, Avira!, MSE, Defender, ZoneAlarm, PC Tools, Comodo, etc.
These messages at startup could be related to some program that has been uninstalled and did not do a good job of cleaning up after itself leaving behind leftover startup entries in your configuration.
Another possibility is malware that was set to run at startup but the referenced file(s) has been deleted after a malware scan leaving behind a registry entry or startup item pointing to a file that does not exist.
It could be from a malicious software removal or an uninstalled application. The entry may have a curious looking name since it was probably generated at random when the malware was installed. If you search your system for the referenced file, you may not even find it.
Windows is trying to load this file but cannot locate it since the file was mostly likely removed during a scan for malicious software. However, an associated orphaned startup parameter or registry entry remains and is telling Windows to load the file when you boot up or login.
You need to remove the referenced entry so Windows stops trying to load or run the file. It may or may not be in the registry but you can find it.
Autoruns (see below) will find the item no matter where it is.
If you just locate and uncheck the item in msconfig, that disables the item but does not remove the reference to the bogus startup item from your computer. The msconfig program is not a startup manager, it is a troubleshooting tool. Disabling things in msconfig to put a stop to the messages and thinking your problem is resolved is short sighted and leaves behind a sloppy Windows configuration. Merely disabling the display of a startup error message should not count as a "solution" to the problem.
If you are comfortable editing the registry you can search for and remove the reference directly from there or remove it using a popular third party tool called Autoruns. The problem may not always be found in the registry though.
Before making any changes to your registry by hand or with third party tools, be sure to make a manual System Restore point just in case. There is no undo or quit without saving option in regedit.
You can use Autoruns to find the leftover startup item no matter where it is hiding. Autoruns does not install anything on your computer. It will display all of the startup locations where the reference might be so you can disable it or delete it completely. Here is the download link for Autoruns:
Launch Autoruns.exe (or Autoruns64.exe for 64-bit systems), maximize the window so you can see everything and wait for it to finish populating the list of entries.
When Autoruns is finished scanning your system, it will say "Ready" at the bottom left corner. Autoruns can be a little intimidating at first if you have never see it before since it displays a lot of information. You are really only interested in a couple sections.
Items that show up in a shrimpy color are "unsigned" entries which are usually not a problem. The manufacturer just did not bother to digitally "sign" their files appropriately.
Items that show up in a yellow color are entries that point to a file, path, location that does not exist so they are suspicious since they probably don't make sense any more. You can choose to delete the yellow ones but sometimes they come back. They probably have nothing to do with your issues since they don't "do" anything.
The problem item is usually in the system startup or user startup entries so click the Logon tab and see if the startup item is there.
Scroll through the list and look for a startup entry related to the file(s) in the error message.
If you don't find it in the Logon tab, look for it in the Everything tab.
You can also click File, Find to search the Logon or Everything tab for all or part of the name of the item.
Right-click on the offending entry and choose to delete it. If you are not sure what it is, you can just disable it, reboot and if the issue is resolved, then delete the offending entry.
If you don't see it in Autoruns you may have to edit the registry and remove the item from the Startup folder there. Autoruns should display the same information though.