See link and multiple reports on VP/T
The inputbox is including HTML and HTML comments into the wiki (as if it is within a <nowiki>, but it isn't ). Removing the "labeltext" option, solves the issue, (but no more labeltext then of course :D )

<inputbox>
type=search2
buttonlabel=Go
labeltext=''Search Wikipedia:''
width=22
id=MP
</inputbox>

Results in:

<i>Search Wikipedia:</i>

<!-- NewPP limit report Preprocessor node count: 6/1000000 Post-expand include size: 0/2048000 bytes Template argument size: 0/2048000 bytes Expensive parser function count: 0/500 -->

En.wp runs: InputBox (Version r42791)

Version: unspecified
Severity: enhancement
URL: http://en.wikipedia.org/w/index.php?title=Wikipedia:Reference_desk/RD_header&oldid=235843235