I've encountered this issue too. However, I suspect the bug exists in bindgraph ability to parse BIND's query log. Bindgraph 0.2 is currently able to parse BIND 9.2 query logs, but BIND 9.3 (including a new query log format) is now in sid.
I've tried simply updating /etc/default/bindgraphfrom LOG_FORMAT=bind92 to LOG_FORMAT=bind93, which had no effect. Perhaps the package maintainer can investigate what needs to be done to parse the BIND 9.3 query log and to add the appropriate measures to check if the system is running BIND 9.2.x of BIND 9.3.y and configure parsing of the appropriate logs.
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