Those modules are working just fine. But they are not the correct modules for your Mac.
Macs are very, very fussy about their RAM. The Mac Pro even more so. Mac Pro uses 72-bit Error-correcting Code (ECC) memory. If present, problems can be detected instantly. Slots 3 and 4 (on each side, if so equipped) in your Mac Pro 4,1 2009 model are shared.
Mac Pro requires substantial heat-spreaders not generally used in modules for other computers, and EPROMs with Apple-approved Temperature sensors.
The module speed has to be adequate. The memory timing has to be just so.
The number of chips on a module has limitations. Certain sizes cannot be mixed with others, except with special buffering. Only certain combinations of buffering and not buffering can be mixed in certain ways.
You can spend months becoming an expert on these issues to support a one-off purchase.
Or you can engage a Mac memory expert. Tell them the Mac Model you have, and they will send you the correct modules for your Mac, "Guaranteed or your money back". And they will throw in a lifetime warranty -- if they ever fail, they will replace the modules at no cost to you.
Here are two Vendors who play by those rules:
If you are not in the US or Canada, post back and readers can make additional recommendations.
mac pro 2.66 quad running 10.5.8. it came with 3 1gb sticks of ram.
Then this is Early 2009 4,1 which has a bug in 10.5.8 only addressed with 10.6.2+ to cause processors to overwork during audio...
The first thing would be to use just the 2x4GB and see if they work, no?
So they don't get along but 8GB works but another 4GB. Your system w 3GB was only barely enough to run basic apps probably.