Jacob,
The underlying assumption on which the success of baseline subtraction is based is that the system is the same except for the signals between the time when the baseline is recorded and the signal is measured. It appears that this assumption is not valid for your application.
Can you post an example of the base line data and an example of the signal data (without the baseline subtraction)? Some people who participate in the Forum are very good at looking at data and proposing suitable methods of analysis.
Lynn
