ibdata file growing huge despite using innodb_file_per_table option

[Nox is]

Hi there, I hope someone can help me shed some light, as this is getting quite urgent.

Mysql version: 5.0.51a-log

root@server:/mysql/data# du -sh *
14M server.err
4.0K server.pid
105G ibdata1
1.0G ib_logfile0
1.0G ib_logfile1
20K innodb_status.20783
20K innodb_status.21314
40K innodb_status.25519
0 my.cnf
760K mysql
0 test
48G monitoring_db

* There has only been single database on this server called "monitoring_db"
* I migrated to this server a month ago, the my.cnf was kept identical apart from increasing buffer pool size as the new server had more ram.
* The old server was version 5.0.45-log - so a minor version increase.
* Old server ibdata1 file did not increase past 978M despite being in service for around 8 months.

My question is what can cause a ibdata file when used in conjunction with innodb_file_per_table to increase so rapidly?

Is there a way to find out exactly what is inside that ibdata file?

Thanks for any help!