GIgabit but only 100mbs?

Try connecting the computers directly to the switch with a known-good cable (as a test).

Have you tested the cables from end-to-end (through the patch panel) to confirm that all 8 wires are properly connected?

Try hardcoding the speed on the switch interfaces the computers are connected  AND/OR check the nic card configuration to make sure they are set to auto and not set to a fixed speed.

What model switch?  And what rating on cabling front and backend?

THe switch is 100% gigabit. I think it's a repunch down issue.  Some of the connections are 1000mb some are not.

Ensure your ethernet card + all gear in your routing chain... set to...

1) Full Duplex.

2) Auto or 1G.

We're sure it's 5e? Quick check is to plug another device with a 1G adapter and roll. Now you know it's the switch and most likely software related. Any version info you can provide?

I'm thinking this is at the PC level but I'm not sure what is going on.  IF I plug in my laptop I connect at 1 g.  The desktops which have 1 g networks are only connecting at 100 mbs.  I've even set it to full duplex 1 gig.  I've tried updating the drivers too.  This is very weird.

When you are testing with your laptop, is it to the same jack with the same cable(s) as the desktops?

From my experience this can also happen with self-terminated cables. 1G depends on the impedance in the UTP cable itself. Each pair is wound / twisted slightly different, and in a certain order.  If you don't pin out to a standard (I use T-568B), or the terminations are not wound (hence not imparting impedance) together enough behind a self-terminated end, the cable is incapable of impedance and falls to 100Mb. Since you have some working, some not, it's at least another thing to look at.

I agree that it is quite possibly a cabling issue.  I'm not at all concerned about impedance at this point until a simple continuity check has been done.  Testers for that are quite inexpensive (under $20) and quick to test.  If a cable fails with that, you know it won't do 1G.  If it passes, then one should look for how carefully they were terminated (or use an expensive tester).

So far I've not read anything here to say we have a good clue that all 8 wires are electrically terminated on the questionable connections.

If OP is getting 100Mb and a connection, it's almost certainly not a continuity issue.  If any of the 4 wires were not continuous it would almost certainly fail even 100mb negotiation.
Having several UTPs with this issue would make continuity issues even more improbable.

I would do 2 things. First i would check the switch ports that are connecting to the desktops. Then I would ask myself what is the rating of the cable running from the patch panel to those desktops. Is it rated at 1Gbps? Let's look at the individual switch ports. Take one that connects to the desktop as a test:

Check your switch. Let's assume the port is 1/1.

Switch-A> (enable) show port capabilities 1/1
Model                    WS-X5530
Port                     1/1
Type                     10/100BaseTX
Speed                    auto,10,100
Duplex                   half,full

Perhaps it is not set correctly:

Configure auto-negotiation for port 1/1:

Issue the set port speed 1/1 auto command to configure auto-negotiation for both speed and duplex mode on port 1/1. Auto is the default for ports that support auto-negotiation.

    Switch-A> (enable) set port speed 1/1 auto
    Port(s) 1/1 speed set to auto detect.
    Switch-A (enable)

Are you plugging your laptop into one of those same wall plates that a desktop uses and getting 1Gbps? When you plug the desktop in does it drop down 100Mbps? Check the NIC settings on the desktop. Set it to auto-negotiate. See what happens then. If still a no go, set it to 1Gbps. What then? If still a no go, set both the port to that desktop to 1Gbps and the NIC to 1Gbps. What happens then?

Any news amigo?

Yes I wound up buying 5 port gig switches for all the PCs and splitting the connections. The phones are in one port and the pc's are in another.  The PCs are running gigabit and the phones are at 100.