Logging from managed packages installed in a subscriber org is currently not visible in the subscriber org's debug logs. It would be simpler for ISV partners to debug and support applications in production if package logging and unhandled exceptions were always logged in the subscriber org.
Package logging would be visible under Setup>Administration Setup>Monitoring>Debug Logs and visible to appropriately permissioned users in the subscriber org. This is where all the other logs are so it would provide execution context.
If you're a developer/ISV partner and DON'T want your logging visible, leave a note in the comments explaining why. Note that what is logged is up to you when you code in Apex, and detailed logging can be removed when you package for production.