On a fresh installation i cannot reproduce this error.
* dev head 25cfdf73
I've tested it using the attached script (must be placed direct in dokuwiki folder and variables on script top needs to be adjusted).
The error message dosn't look xml-rpc specific. It looks like your http client has a fixed timeout of 15sec and the server isn't able to respond in that time.
IMHO this is an performance problem. I guess your wiki contains a lot of pages/content. So calls that affect a lot of data are may to slow for that timeout.
The dokuwiki.getPagelist command has to a lot of data and the wiki.putPage has to update the search index.