curious if my behaviour caused loss of face?

I was coming back from Hanno one night and the train stopped at a station and didn't move for a good hour. All announcements were in Japanese, to my disadvantage. Most people just left the train. When I got into Ikebukoro I approached one of the few staff members that I could see and tried to explain that the train was very late and whether there was something in place that would pay for my taxi fare back to the hotel. I didn't sound angry, but I think I was kind of insistent and looking back, they just stared at my phone (showing them the connection) and looked at each other for what seemed like ten minutes.

I gave up and was relieved that my taxi fare was only y4000. I do recall the guys laughing after I left and said "taxi" in english. I feel pretty bad about all this, I put them in an uncomfortable situation and made myself look like a typical baka gaijin :P I realise that it wasn't that big a deal and that other foreigners probably do worse all the time, but what may they have made of the way I acted?

Since I am not a witness, I can only guess what happened, but it doesn't seem like you did anything wrong or stupid or made them feel needlessly uncomfortable.

When you say "they just stared at my phone (showing them the connection)", are you talking about train connections? If so, I'm pretty sure they thought you were trying to find public transportation that can take you to your destination. And since you suggest that there were more than one staff dealing with you, it sounds like they were trying to get as much help to assist you since you probably seemed pretty lost. It's natural to assume that they laughed because they were relieved to learn that you found your way home, which was a taxi. All these are guesses, though.

By the way, each railway company has regulations concerning train delay. If it's a big delay, you can usually have a "furikae-yusou-hyou" 振替乗車票 issued, which is a slip that will allow you to ride certain alternative trains or buses for free. This normally does not include the use of taxis.

Sudden annoucements like these are almost always done only in the local language (which I find is similar in all countries I've traveled to). Next time, you should start asking a station staff before it becomes too late to catch any public transportion. At least you can find a conductor at the very rear of your train. There will always be an alarm before the door closes, so until you hear it you can take your time to walk to the conductor and ask "how long the train stops". If it seems long enough, you should go to the ticket gate for more details.

Again, the delay and language barrier are not your fault, and even locals often end up discussing with the train staff only to fetch a cab by themselves. So although it was an unfortunate incident for you, I don't think you caused any loss of face. I can only hope that if the conversation became any longer they would have contacted an interpretation service they might have.

Hope you enjoy the rest of your stay in Tokyo.

I suggest reporting Seibu Railway (?) all that happened specifying time/date/place and asking for clarification.
http://www.seibu-group.co.jp/railways/tourist/english/cs/

This is actually something that happened on my last visit, and I didn't seem to mention that I missed the last subway (due to the Hanno train being so late). I was more thinking that my pointing out this flaw in public to train staff would have been embarrassing for them.

Oh, and the (excellent) english-speaking staff at my hotel told me they hadn't heard of any agreement to reimburse for taxi fares so I just didn't worry about it. It was a bit penny-pinching now I think of it, even though that's 20% of my weekly income.

what you mean in this thread ?
you took the last train and you failed to take the next connecting train, because of the delay of the previous train.
in that case, the company will not pay your loss, because they don't promise the on-time running.

This is a tranlation of the gist of the thread:
トピ主さんが言いたいのは、「事が起きた当時、自分は駅員に迷惑をかけてしまったのではないか、自分はバカなガイジンだと思われたんじゃないか、でもそれほど気にすることはないのかな、どう思われたんだろう。もう遥か、前回の訪日の話ではあるけれど気になったもんで」という内容ですので、特に改善策がないのならスルーでいいと思います。