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It looks as if the tick box Configure=>Synchronize does not work properly, but the key shortcut for the command does.

Heres another odd thing:
With vertical scroll off before horizontal split, split horizontal then turn on vertical scroll.
This only gives a scroll bar in one of the splits.
Now ...

[quote="helios"]Have you tried disabling the Synchronize Scrolling option from the Configure menu? It works for me.[/quote]

Assuredly it does not work (certainly not in XP classic).

Synchronization is off.

Tried Tabs on/off and horizontal scrollbar on/off as well. Same result.

Horizontal ...

If the window is split vertically then both panes are synchronized when scrolling vertically.

Is there any way to disable the synchronization?

On w2k virtual machine, all settings classic (NT look and feel), 5.4 works as expected.
On xp32 host machine, all settings classic (NT look and feel), 5.4 exhibits the same problematic check boxes.

Hope this helps.