I have a custom userdata and cache location for my Chrome, it's in the F:\Temp folder on a secondary drive.
Unless I add Chrome flags to the cache location my bookmarks bar and bookmarks etc. don't load.
Here's the fix.
Note after adding the flags I had to change the GroupMax to 0 or they'd open up in two separate groups.
I tried just adding that location to the appropriate entry in my registry for Chrome but bookmarks still wouldn't load until I did this.
Here's a link to how my Groupy looks when done. 
https://imgur.com/a/dnzCM1z
[GroupyEntry1]
OwnerProcess=C:\Windows\explorer.exe
RunElevated=0
Target="D:\"
MatchingClass=CabinetWClass
[GroupyEntry2]
OwnerProcess=C:\Windows\explorer.exe
RunElevated=0
Target="D:\Drivers"
MatchingClass=CabinetWClass
[GroupyEntry3]
OwnerProcess=C:\Windows\explorer.exe
RunElevated=0
Target="F:\"
MatchingClass=CabinetWClass
[GroupyEntry4]
OwnerProcess=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
RunElevated=0
NoPatternMatching=0
CommandLine= --new-window https://www.win-raid.com/t29f25-Recommended-AHCI-RAID-and-NVMe-Drivers.html --user-data-dir="F:\Temp" --disk-cache-dir="F:\Temp" -- "%1"
WorkingDirectory=C:\Program Files (x86)\Google\Chrome\Application
Target=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
MatchingClass=Chrome_WidgetWin_1
[GroupyEntry5]
OwnerProcess=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
RunElevated=0
NoPatternMatching=0
CommandLine= --new-window https://www.win-raid.com/t596f39-Intel-Management-Engine-Drivers-Firmware-amp-System-Tools.html --user-data-dir="F:\Temp" --disk-cache-dir="F:\Temp" -- "%1"
WorkingDirectory=C:\Program Files (x86)\Google\Chrome\Application
Target=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
MatchingClass=Chrome_WidgetWin_1
[GroupyEntry6]
OwnerProcess=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
RunElevated=0
NoPatternMatching=0
CommandLine= --new-window https://www.win-raid.com/t895f42-Intel-Chipset-Device-quot-Drivers-quot-INF-files.html --user-data-dir="F:\Temp" --disk-cache-dir="F:\Temp" -- "%1"
WorkingDirectory=C:\Program Files (x86)\Google\Chrome\Application
Target=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
MatchingClass=Chrome_WidgetWin_1
[GroupyEntry7]
OwnerProcess=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
NoPatternMatching=0
CommandLine= --new-window https://downloadcenter.intel.com/download/22283/Intel-Ethernet-Adapter-Complete-Driver-Pack --user-data-dir="F:\Temp" --disk-cache-dir="F:\Temp" -- "%1"
WorkingDirectory=C:\Program Files (x86)\Google\Chrome\Application
Target=C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
MatchingClass=Chrome_WidgetWin_1
[Group]
GroupCount=7
GroupLeft=0
GroupTop=0
GroupRight=2574
GroupBottom=2174
GroupMax=0