Try asking on the Flash Builder forum.
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Modules are currently inefficient to compile, because source files shared between modules and the main app are recompiled for each module. We will be addressing this in the upcoming "Hero" release. In the meantime, you could try moving common source files into a SWC. Also consider precompiling your font into a SWF and then embedding the transcoded font symbol from the SWF; this will avoid the font being transcoded each time you compile.
Adobe Flex SDK Team
I have the same problem (having 12 modules) and incremental compilation is set to true but still it takes 1-2 minutes. This is highly unproductive, please help!
When embedding fonts, specify the unicode range so the compiler doesn't have to embedd the entire font file. Also if you set advanced-anti-aliasing to false (this is set to true by default), you should see font embedding go a little faster.
Also as Gordon mentioned, module compilation scenario was optimized in the upcoming Hero release.
Flex SDK Team