It could happen that on CQ5.5 SP2 after restarting the instance you see the CRX welcome page and not the CQ one.
This is due to the fact that within the repository there are two Sling vanity paths both referencing ‘/welcome’. The sling:VanityOrder is 200 for CQ and 900 for the CRX one. The higher wins.
you can find the nodes by doing a search in CrxDE Lite.
SELECT * FROM [nt:base] AS s WHERE s.[sling:vanityPath] = '/welcome'
To solve once and for all the issue I remove the sling:vanityPath property from /libs/crx/core/content/welcome. Another option could be by changing the vanityOrder to something lower than 200.
It should not happen in 5.5 SP2.1 but in case this is how I went around it.