http://confluence.atlassian.com/display/JIRA043/Advanced+Searching?clicked=jirahelp#AdvancedSearching-ReservedCharacters claims:

If you wish to use these characters in queries, you need to:

• surround them with quote-marks (you can use either single quote-marks (') or double quote-marks (")); and
• precede them with two backslashes.

For example: summary ~ "\\[example
]"

So, to search for version "4.3 - EAP", one would have to enter:

 
fixVersion = "4\\.3\\ -\\ EAP"

However, this results in an error:

 
The value '4\.3\ -\ EAP' does not exist for the field 'fixVersion'.

Correct is to use quoted strings, but NOT a double backslash:

 
fixVersion = "4.3 - EAP"