Of English? Yeah, I guess so. I'd say 'often' should be either the second word here, or the last one. In Polish as well, plus "on lata często".
I think you were right in the first place. I doubt a native English speaker would say "He flies often to the capital" it may be grammatically correct but it is not fluent.
The usual position for adverbs of frequency is before the main verb, "he often flies ..." and unless you're up to native-speaker standard it's advisable to stick with this.
It can sometimes go at the beginning or right at the end, "He flies to the capital quite often", or "He flies quite often". But we don't separate the verb "go" from its destination "to the capital".
I cannot check now, but if you hear 'czasto', that's not how it should sound. ę = eu, roughly.