It could be something plugin-specific, but if it's an issue with multiple announcements, I imagine that it's probably a template issue. I know my announcements plugin looks for one of the notifications in the header and adds the template variable after that. I imagine the others probably do the same thing, so if you have a highly modified header design, that could be part of the issue.
For OUGC Announcement Bars, it looks like "<!--OUGC_ANNBARS-->" is needed somewhere after the navigation section of the template. If that's not found, try putting it at the bottom of the header template.
For my plugin, ""<!-- BAM -->{$bam_announcements}<!-- /BAM -->" is the variable that is used, and can be added anywhere in the header that you prefer (by default is after {$awaitingusers}). The "Announcement" plugin uses the {$announcement} variable, which is by default placed before the pm_notice variable in the header template.