These are known problems of PolyGlot v1.4 as described by Fabien Letouzey.
The addition of Chess960 support lead to a change in internal-move representation for castling. This slightly affected the opening-book format. We recommend that you recompile books with this version.
Several users reported engines losing on time. The playing conditions always mixed playing on an Internet server with pondering.
It is not yet clear what the source of the problem is, but there seems to be a forever incompatibility between the xboard and UCI protocol regarding a complex pondering/remaining-time relation.