Mac mini will only boot in safe mode ~

I need help with my mid-2011 mini. I purchased this used and it worked fine for the day I had it set up before installing OS Sierra. It was wiped clean when I acquired it.
Here are the specs:

Macintosh HD:

Available: 487.61 GB (487,606,030,336 bytes)

Capacity: 499.25 GB (499,248,103,424 bytes)

Mount Point: /

File System: Journaled HFS+

Writable: Yes

Ignore Ownership: No

BSD Name: disk0s2

Volume UUID: DF680B65-09AE-31C0-AB02-626D159B3A6C

Physical Drive:

Device Name: TOSHIBA MK5065GSXF

Media Name: TOSHIBA MK5065GSXF Media

Medium Type: Rotational

Protocol: SATA

Internal: Yes

Partition Map Type: GPT (GUID Partition Table)

S.M.A.R.T. Status: Verified

Now, upon installing Sierra, I get a black screen, sometimes with just the mouse visible. Sometimes, after multiple reboots on its own, or with me doing it manually, it will boot to the desktop, but the menu bar is missing and I cannot click on anything.

In safe mode, it works fine. Running Disk Utility on the Toshiba, while in safe mode, gives me the following:

Checking prerequisites

Checking the partition list

Checking the partition map size

Checking for an EFI system partition

Checking the EFI system partition’s size

Checking the EFI system partition’s file system

Checking the EFI system partition’s folder content

Problems were found with the partition map which might prevent booting

Operation successful.

It says to repair the start up volume I need to run Disk Utility in Recovery mode.
When I use Disk Utility in Recovery mode it finds no issues!

I have also tried reinstalling Sierra from Recovery mode but this results in the same booting troubles.

Per other posts, I have downloaded and installed EtreCheck. This is the only download or change I've made to the system. I haven't even set up iCloud.

EtreCheck results:

EtreCheck version: 3.4.4 (448)

Report generated 2017-08-31 12:13:42

Download EtreCheck from https://etrecheck.com

Runtime: 4:11

Performance: Good

Click the [Lookup] links for more information from Apple Support Communities.

Click the [Details] links for more information about that line.

Click the [Clean up] link to delete unused files.

Problem: Other problem

Description:

Will not boot Sierra when not in Safe Mode

Hardware Information: ⓘ

Mac mini (Mid 2011)

[Technical Specifications] - [User Guide] - [Warranty & Service]

Mac mini - model: Macmini5,1

1 2.3 GHz Intel Core i5 (i5-2415M) CPU: 2-core

8 GB RAM Upgradeable - [Instructions]

BANK 0/DIMM0

4 GB DDR3 1067 MHz ok

BANK 1/DIMM0

4 GB DDR3 1067 MHz ok

Handoff/Airdrop2: not supported

Wireless: en1: 802.11 a/b/g/n

Video Information: ⓘ

Intel HD Graphics 3000 - VRAM: 512 MB

HP 2009 1600 x 900 @ 60 Hz

Disk Information: ⓘ

TOSHIBA MK5065GSXF disk0: (500.11 GB) (Rotational)

[Show SMART report]

EFI (disk0s1 - MS-DOS FAT32) <not mounted> [EFI]: 210 MB

Macintosh HD (disk0s2 - Journaled HFS+) / [Startup]: 499.25 GB (487.57 GB free)

Recovery HD (disk0s3 - Journaled HFS+) <not mounted> [Recovery]: 650 MB

USB Information: ⓘ

USB20Bus

hub_device

Apple Inc. BRCM20702 Hub

Apple Inc. Bluetooth USB Host Controller

USB20Bus

hub_device

Apple Computer, Inc. IR Receiver

Thunderbolt Information: ⓘ

Apple Inc. thunderbolt_bus

System Software: ⓘ

macOS Sierra 10.12.6 (16G29) - Time since boot: less than an hour

Gatekeeper: ⓘ

Mac App Store and identified developers

Clean up: ⓘ

~/Library/LaunchAgents/com.apple.CSConfigDotMacCert-[redacted]@me.com-SharedSer vices.Agent.plist

/System/Library/Frameworks/CoreServices.framework/Frameworks/OSServices.framewo rk/Versions/A/Support/CSConfigDotMacCert -l ~/Library/Logs/CSConfigDotMacCert.log -u [redacted]@me.com -t SharedServices -s

Executable not found!

One orphan file found. [Clean up]

System Launch Agents: ⓘ

[not loaded] 8 Apple tasks

[loaded] 190 Apple tasks

[running] 84 Apple tasks

System Launch Daemons: ⓘ

[failed] com.apple.ucupdate.plist (Apple, Inc. - installed 2017-07-15)

[failed] com.apple.watchdogd.plist (Apple, Inc. - installed 2017-07-15)

[not loaded] 40 Apple tasks

[loaded] 180 Apple tasks

[running] 95 Apple tasks

Launch Daemons: ⓘ

[not loaded] com.apple.installer.osmessagetracing.plist (Apple, Inc. - installed 2017-07-15)

User Launch Agents: ⓘ

[not loaded] com.apple.AddressBook.ScheduledSync.PHXCardDAVSource.E9767781-F916-41A1-AC9A-2B4 A58B13F46.plist (Apple, Inc. - installed 2017-08-30)

[not loaded] com.apple.CSConfigDotMacCert-[redacted]@me.com-SharedServices.Agent.plist (? ? ? - installed 2017-08-29) - /System/Library/Frameworks/CoreServices.framework/Frameworks/OSServices.framewo rk/Versions/A/Support/CSConfigDotMacCert: Executable not found!

Internet Plug-ins: ⓘ

QuickTime Plugin: 7.7.3 (installed 2017-07-15)

3rd Party Preference Panes: ⓘ

None

Time Machine: ⓘ

Time Machine not configured!

Top Processes by CPU: ⓘ

4% WindowServer

1% syncdefaultsd

0% fontd

0% com.apple.WebKit.Networking

0% kernel_task