(I am using version 3.5.0)
If you have an apostrophe in an SQL comment, SQuirreL does not seem to recognize any parameters on any following lines. The following SQL code illustrates the problem. SQuirreL sends the code straight to the JDBC driver without prompting for a value for :zip. Remove the apostrophe, and it finds the :zip parameter.
-- the ' in this comment keeps SQuirreL from finding the :zip parameter
WHERE ZipCode = :zip
SQuirreL is an awesome tool. I happened to notice a peculiar but reproducible bug, so I thought I would submit it. I realize that this issue is probably not a high priority.