There are several known issues with this modpack:
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Optifine set to multi-core loading (strongly recommended!) can cause flickering of chunks. This is a known issue with Optifine and NVidia cards. To solve it disable "threaded optimizations" in the NVidia control panel. You can find more information on this issue on the Optifine page.
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Thaumcraft leaves cause significant lag. This is a known bug that will not be fixed by the autor of Thaumcraft. You can either cut down all greatwood trees in sight, or wait a few minutes till the leaves calculation is done. Optifine should take care of most of the lag, but still - depending on your machine - things might slow down in mystical forests.
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Gravestones and especially backpacks might end up in strange locations. If you die and cannot find your backpack again, don't give up too early. They might just be a few blocks below your grave in a cave you haven't seen before. In 99.9% of all cases your stuff is save.
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Sometimes when clicking graves items might end up in your armor slot. This is a forge bug that is most likely not going to be fixed. Just take them off your armor slots to return them to your inventory.
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Server owners running public servers might consider removing Archimedes Ships, as this is a very easy way to grief structures.