Okay, here is a little bit more info.

                   H
                   | 
B----C             G
|   /              |
A  /               F
| /                |
D-------FIBER------E

A is root for vlan 2-999 on every switch.
A is root for vlan 1 on A, B, C and D.
E is root for vlan 1 on E, F, G and H.

The second fiber (which is not active at the moment)
connects C and H.

When the second fiber is activated a broadcast storm
starts within 60 seconds.

--- ooo ---

A, B:             WS-C2950T-24

C, D, E, F, G, H: WS-C3560G-24TS

--- ooo ---

Below I have pasted the important part of
every conf (I hope!):

A

spanning-tree mode pvst
no spanning-tree optimize bpdu transmission
spanning-tree extend system-id
spanning-tree vlan 1-999 priority 8192

B

spanning-tree mode pvst
no spanning-tree optimize bpdu transmission
spanning-tree extend system-id
spanning-tree uplinkfast

C

spanning-tree mode pvst
no spanning-tree optimize bpdu transmission
spanning-tree extend system-id

D

spanning-tree mode pvst
spanning-tree extend system-id
spanning-tree vlan 1-999 priority 49152

E

spanning-tree mode pvst
spanning-tree extend system-id
spanning-tree vlan 1-999 priority 40960

F

spanning-tree mode pvst
spanning-tree extend system-id
spanning-tree vlan 1-999 priority 49152

G

spanning-tree mode pvst
spanning-tree extend system-id
spanning-tree vlan 1-999 priority 49152

H

spanning-tree mode pvst
spanning-tree extend system-id
spanning-tree vlan 1-999 priority 49152

--- ooo ---

A#show spanning-tree root

                                        Root Hello Max Fwd
Vlan                   Root ID          Cost  Time Age Dly  Root Port
---------------- -------------------- ------ ----- --- ---  ----------------
VLAN0001          8193 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0002          8194 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0003          8195 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0004          8196 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0005          8197 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0007          8199 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0008          8200 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0016          8208 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0023          8215 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0024          8216 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0025          8217 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0032          8224 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0033          8225 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0034          8226 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0300          8492 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0301          8493 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0302          8494 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0444          8636 0013.1a5d.08c0      8    2   20  15  Gi0/20
VLAN0999          9191 0013.1a5d.08c0      8    2   20  15  Gi0/20

--- ooo ---

E#show spanning-tree root

                                        Root    Hello Max Fwd
Vlan                   Root ID          Cost    Time  Age Dly  Root Port
---------------- -------------------- --------- ----- --- ---  ------------
VLAN0001         40961 0017.e010.4f80         0    2   20  15
VLAN0002          8194 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0003          8195 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0004          8196 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0005          8197 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0007          8199 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0008          8200 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0016          8208 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0023          8215 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0024          8216 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0025          8217 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0032          8224 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0033          8225 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0034          8226 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0300          8492 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0301          8493 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0302          8494 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0444          8636 0013.1a5d.08c0         8    2   20  15  Gi0/28
VLAN0999          9191 0013.1a5d.08c0         8    2   20  15  Gi0/28

--- ooo ---

Finally, here is the interface part from the conf where 2 switches
are connected:

A, B:

interface GigabitEthernet0/x
 description xxxxxx
 switchport mode trunk


C, D, E, F, G, H:

interface GigabitEthernet0/x
 description xxxxxx
 switchport trunk encapsulation dot1q
 switchport mode trunk