Processing many objects taking too long

[Claire]

My application has a thread reading byte[] arrays from an unmanaged
dll(realtime controller monitoring). The array represents an unmanaged
struct containing a series of header fields plus a variable sized array of
upto 300 structs. Current version of c# doesn't support this sort of struct
hence I just pass an array of bytes to the dll.
When I read these in, I use a binaryreader to process the data to fill out
the c# instance of my class representing this data.
Then the list of objects is appended to another list ready for processing by
another thread.
The processing of this 2nd list can take some time as the list of objects is
compared to a list of equal size eg a 300*300 matrix to see if the data
should be sent to the database.
This takes a long long time, and is much slower than the first thread
grabbing data. There's a bottleneck and I need to speed up this 2nd level
processing.
Does anyone have any ideas on how I can speed this up?
Should I not do the conversion of the byte arrays and instead read straight
from the array? Should I write a c++ dll?
thanks