Even if something wasn't installed in the ideal location, as long as everything can be found, that shouldn't be an issue.

Corrupted paths are a common issue in High Sierra and Mojave. A Safe Boot fixes that and restores the caches to default. Pre OS X, this called Rebuild Desktop and was done the same way. Frankly, I don't expect it to have an effect but it's still good maintenance. This has fixed a number of annoying issues on my and my client's machines including generic alias icons:

Shut down. Boot while holding the Shift key. Log into your User account when prompted. When your desktop icons have finished rebuilding, shut down again. Boot normally.

Assuming that the SSD is healthy and not too full, the normal culprits are (a) an old bit of code that is trying to load and failing thus interfering with the process or (b) something is missing having been overwritten by something else and the OS keeps trying before giving up and moving on.

Either of these can be seen in Console.app. Every process is time stamped. Sometimes you have to drill down to get a good look. Look for something that keeps trying to load but can't or something that BIAB keeps looking for and can't find.

I've had problems with such garbage as 2005 HP print drivers trying to load in Logic, Finale 2009 Help files crashing Time Machine in 2014, Mackie HUI drivers failing to load slowing down Digital Performer... the list goes on.

BIAB 2024 Audiophile Mac
24Core/60CoreGPU M2 MacStudioUltra/8TB/192GB Sequoia, M1 MBAir, 2012 MBP
Digital Performer11, LogicPro, Finale27/Dorico/Encore/SmartScorePro64/Notion6 /Overture5