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I experience this problem even when the second graph imported is static. i.e. enabling the timeline seems to freeze Gephi when any other graph is loaded.
(My system: Product Version: Gephi 0.8.2 201210100934
Java: 1.6.0_65; Java HotSpot(TM) 64-Bit Server VM 20.65-b04-462
System: Mac OS X version 10.6.8 running on x86_64; MacRoman; en_US (gephi))
Way to reproduce:
The UI gets frozen
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