decreased performance of stored procedure when migrated from mysql server 5.0 to 5.5

[michael lando]

i recently testing the move of our db from one server to another.
as part of this process i copied all the data to the new db and started testing it.
as a comparison i run a store procedure whose execution on the old DB took about 2.5 hours on the new db it took about 8.
now the amount of data is the same and the sp is the same the differences is in:
old db
mysql version 5.0.45
pc
OS Name Microsoft Windows XP Professional
Version 5.1.2600 Service Pack 3 Build 2600
Processor x86 Family 6 Model 15 Stepping 13 GenuineIntel ~2394 Mhz
Total Physical Memory 2,048.00 MB

new db
mysql version 5.5.25a
pc

OS Name Microsoft(R) Windows(R) Server 2003, Standard Edition
Version 5.2.3790 Service Pack 2 Build 3790
System Manufacturer Dell Inc.
System Model PowerEdge 2900
System Type X86-based PC
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Processor x86 Family 6 Model 15 Stepping 11 GenuineIntel ~1862 Mhz
Total Physical Memory 4,090.64 MB

if any one has any idea what to check i will be happy to hear.