"Up the pole an' 'alf-way round the flag", in more standard writing is "up the pole and half-way around the flag". "Up the flag"pole" is UK slang for insane. The part about being "half-way around the flag" does not appear to be a common phrase, but rather, it serves as an extension of the previous expression and intensifies it.
"Ideez fix" is an intentional misspelling of "idée fixe" -- an "obsession", or an idea that dominates the mind. It is intentionally misspelled, to highlight the informality of the conversation, as well as the speaker's unfamiliarity with the actual phrase.
"What they talk about" is informal and humorous, and can be interpreted as "that they talk about".
So, to summarize, the subordinate thinks that Pender is insane, and has what some people call an idée fixe -- an obsession.