These behaviours are actually by design. Both the /flash and blink features have evolved over time based on feedback, so the help file needs to be updated in that regard.
The /flash command only displays a custom message if you flash the main mIRC window. If you use it to flash any other window, it will display [message waiting].
The switchbar "blink icons" feature has a number of exceptions, all of which depend on context. For example, it will never blink custom window icons, it will only blink highlighted channel/query window icons, and so on.
Update: I think I can change the behaviour to make it more consistent, eg. if you are /flashing an MDI window, the message should still be displayed in the mIRC titlebar and the switchbar icon should still blink. These changes will be in the next version.
