@Tom Thanks for posting in our Q&A. From your description, did you mean that when you logged back, the start menu layout is changed to its default setting? If there is anything misunderstanding, please correct me.
For this issue, it is suggested to check some information:
1.Please check if the policy deployment status shows succeed in intune portal.
2.Please check the registry key "HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Advanced\Start_Layout"
0 = Default
1 = More pins
2 = More recommendations
If there is anything update, feel free to let us know.
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