MySQL lost records in a master slave scheme
My guess would be that there are three(3) aspects to look over:
ASPECT #1
I would be concerned with InnoDB settings because there are new features in InnoDB (starting with the plugin as of MySQL 5.1.38) that allow for accessing multiple CPUs. If you do not set the parameters, InnoDB will behave like it did before the enhancements. In fact, there are cases where InnoDB in older versions of MySQL will operate faster than newer version:

How do I properly perform a MySQL bake-off?
Why mysql 5.5 slower than 5.1 (linux,using mysqlslap)
Using multiple cores for single MySQL queries on Debian
Is the CPU performance relevant for a database server?

ASPECT #2
I would be very carful when upgrading MySQL 5.1 to another version of MySQL 5.1 because MySQL 5.1 introduced the concept of installing plugins because you now have the table mysql.plugin. If you install a newer version of MySQL, make sure you do not hose mysql.plugin. You have to just reinstall the plugin. This, in itself, is not the cause of your problem. Nevertheless, you need to be aware of this in the event that this is a cause.
ASPECT #3
If you have not already done this, I would raise innodb_log_buffer_size to 32M. The default is 8M. Increasing it will reduce disk I/O. Please do not go beyond this, since large COMMITs can and will form I/O-based bottlenecks.
RECOMMENDATION
I would upgrade completely to MySQL 5.5 because all of the InnoDB Plugin is natively installed in MySQL 5.5. As highlighted in my previous links, you must configure and tune the settings needed for InnoDB to use multiple CPUs. Increase your log buffer
UPDATE 2012-06-03 18:30 EDT
Since you cannot install MySQL 5.5, you still have aspects 2 and 3 you could implement.

Install the InnoDB Plugin
Increase the innodb_log_buffer_size to 32M