Why is my Mac mini starting up very slowly?

You're right that the report is pretty clean. I would only have a few suggestions, based on it:

• Your Mac is currently running macOS Sonoma 14.7.1 (at least at the time the report was run.) I suggest updating it to 14.7.4 (currently the latest available.)
• Your Mac appears to still be running some iTunes components. I'm sure you are aware that Apple replaced iTunes with three separate apps: Music, Podcasts, & TV, with the release of macOS Catalina. Not necessarily an issue, just an observation.
• Your Mac is running CleverFiles' backup service. I am aware of this app, but am not fully familiar with it. If it is configured to run in the background, it may be one reason for the slow startups.
• It appears that you are either currently using a number of printers or some of the by the number of kernel extensions / printer drivers (kexts) in the report. If you are not still using all of these, you may want to clean up your current available printers.
• The com.ninxsoft.mist.helper.plist file is associated with Mist, a macOS utility developed by Ninxsoft. If I understand what this does, I believe it is used to automate the process of downloading macOS firmware and installers, offering features such as listing available macOS versions, downloading firmware restore files for Apple Silicon Macs, and creating various installer formats for Intel-based Macs. Sounds interesting, but I'm not sure how this may, or may not, affect your Mac's boot up performance.
• Looks like you are using a couple of VM managers: virtualbox & VMware. Shouldn't affect startup performance.
• I see that you are using an app cleaner, called SmartDelete. These are really not needed, and tend to cause more issues than resolve them. It's totally your call, but I would suggest that you consider completely removing this one.
• Auto Launcher Reverso - I couldn't find anything about this app so I can really comment on it. Although I don't think it would affect start up performance.
• None of the current High CPU Use issues, under the Diagnostics Information section, except the last one (apfsd High CPU Use), is a major concern. High CPU usage by apfsd (Apple File System Daemon) usually means your system is working hard to manage APFS-related tasks, which are typically tied to disk activity. apfsd is responsible for handling all interactions with APFS volumes — so when it spikes, it's often reacting to something that’s touching the disk frequently or in large volumes. The most common causes for these are:
  • Spotlight Indexing
  • Time Machine
  • Heavy disk activity apps ... like VM managers. Probably the cause here.
  • File system corruption or errors.

Besides the report result, I want to make sure of a few thing, so please bear with me as I ask a few more questions:

• Is the Kingston XS1000 the external SSD that you are booting from when you experiencing these slow start up times?
• When booting directly from your mini's internal drive, does it still boot up slowly?

The repeated mach-lookup deny messages from com.apple.WebKit.WebContent trying to access com.apple.diagnosticd are likely a red herring. These sandbox denial messages are typically harmless and expected under macOS’s hardened runtime and sandboxing model, especially with WebKit and system daemons. They get logged a lot, but they don't usually correlate with performance issues — especially not the kind that would slow down a boot by 10 minutes. So while it clutters the logs, that’s probably not your culprit.

What is more likely is that something is stalling early in the boot process — either a system extension, a launch agent/daemon, or some file system issue. The fact that Safe Mode doesn’t trigger correctly is interesting too, because Safe Mode should disable third-party launch agents, non-essential kernel extensions, and do a directory check of your startup volume. If it's failing to enter Safe Mode (as in, no red text on the login screen and regular startup behavior), it could indicate:

• A firmware/SMC-related issue
• External peripherals interfering (especially if you've got USB hubs or external drives connected)
• Or third-party software that’s hooking into early boot in a weird way (like antivirus, VPNs, or system-monitoring tools)

At this point, I would suggest that you run an Etrecheck report, and optionally, post it here if you need assistance with interpreting its results.

Ref: Using EtreCheck to Troubleshoot Potential Mac Issues

Have you tried either, to see if either make a difference:

• Connecting the external drive directly to your mini?
• Still using the hub, but removing the other devices, leaving only the external boot drive connected?

Richard Groff2 wrote:

I used Retroactive to reinstall iTunes, which I much prefer to the newer Music app. This will keep me at Sonoma, on this Mac anyway (I have 7 altogether, used for different purposes).

Interesting, I will have to check that out myself for some of my older Macs.

I'm going to have to research CleverFiles. It doesn't ring a bell and a search of my Mac shows nothing.

cleverfiles is the author of Disk Drill, a popular file recovery app. Does that help "ring a bell?"

And yes, the 2TB Kingston SSD is what I'm booting from. The internal 250GB HD is being used for music and photo backups of my phone and isn't bootable.

Ah, ok. As you are probably already aware, booting up from an external drive is never going to have the same performance as from the internal one. Your 2018 mini is a very capable computer. I had one a while back. Based on what hardware is installed on it, I can see why you needed to unload some of your files/apps to an external drive. However, I think you will be far more satisfied with it performance, if you use its internal drive as the boot drive, and then, use a large external drive or NAS for your file storage.

To put it into perspective, there are a number of processes that take place when your Mac boots up. Most of the latter ones require access to the system drive (normally). With this drive being external, it will cause delays. What may have increased these delays may be due to additional apps that you are running that need to start up during the boot process. Anyways, it's your call. With as many Macs as you have, it certainly is fun to "play" around with them.