I agree with your theory, that Pipes could be rate limited to your source OR your source actually is having serving issues every now and then.
When this kind of thing happens I tend to feedburn the feed and use the feedburner rss url to fetch the rss instead of the original source. Feedburner effectively becomes a proxy - providing caching and stability.
yeah I've also been having problems with this. I tried the feedburner idea but get the error . Weird thing is when i run pipe everything looks good. When i try the rss feed nothing works. I think i'm just going to stick with chimpfeedr. oh well.