I cannot tell you exactly what is happening without looking at the configs of the Switches and the WLC you have as I can think of a number of possibilities. For me, it'd be helpful to have that information but more so, the things that you've done. Basically, what are the items you've tried thus far?
SW-A: 10.133.55.1 <---TRUNK---> SW-B: 10.133.55.2
WLC-4404 10.128.55.10
First thoughts though are as follows:
1.) Who is able to ping the WLC?
a.) no one = check the interface on the switch and the WLC interface config, any firewalls
b.) same subnet, 10.128.55.0/24, but no other subnets = check routing
c.) all subnets on one switch but not from another switch = check trunk on SW-A & SW-B
2.) AP and WLC are able to ping each other but AP not showing up in WLC
a.) check DHCP has the proper option 43 (Vendor Specific Info) set which tells the AP what IP the WLC is.
b.) check any firewalls inbetween
c.) create new interface on WLC with the same VLAN subnet as the AP and test
d.) enable ssh on the AP and do a show log to see if anything peculiar sticks out
3.) You've checked all possibilities and as the config stands everything should work
a.) reload the switches, AP's, WLC
b.) pull out the configuration and put the configuration back in specific to the issue
c.) try a different interface on the switch for the WLC
d.) try a different interface on the WLC (maybe create a new one)
e.) get on Cisco.com and use the bugtoolkit to see what bugs are out there for your particular WLC version.
f.) upgrade the WLC version a revision up and test.
I realize that some of my ideas are not really applicable, but I'm just throwing some ideas out there to maybe help give a new perspective on the problem. I've found just taking a break to think about something else and then coming back helps me.
Best Answer
Converting comments to an answer.
We've had problems regarding software upgrades via Prime on new equipment, like the 3650, 3850, 9000 Series from Cisco. Prime is not setting the bootvar correctly and often, this results in the switch not being able to boot or not being upgraded i.e. rebooting on the old software. We've created a TAC case with Cisco, but it's low priority.
We haven't had problems with the 2960S/X series luckily. We have about 2000 of these and they've not produced any problems when using Prime to upgrade them. Last time 1% didn't work, but that was hardware related. The only flaw to note is when Prime tries to upgrade this type of switch and the flash is full. This will generate an error while deploying fortunately.
I'm pretty confident, that you can upgrade your 2960S/X series without any problems.