Here my stats on the gems i made. I'll update these with Huge Citrine, Bloodstone, and Sun Crystal tonight/tomorow.
229x [Chalcedony]
Perfect: 45
Normal: 184
% that did become perfect: 19,65%
Price of gems: 114,5g
Gold when sell all gems to vendor: 137g
Profit: 22,5g
207x [Dark Jade]
Perfect: 43
Normal: 164
% that did become perfect: 20,77%
Price of gems: 103,5g
Gold when sell all gems to vendor: 125g
Profit: 21,5g
253x [Shadow Crystal]
Perfect: 59
Normal: 194
% that did become perfect: 23,32%
Price of gems: 126,5g
Gold when sell all gems to vendor: 156g
Profit: 29,5g
Stats on all gems together:
Total Gems: 689
Total Perfect: 149
Total Normal: 542
Total % that did become perfect: 21,62%
Total price of all gems: 344,5g
Total gold when sell all gems to vendor: 420g
Total profit: 75,5g
So, i would say that the chance to get a perfect gem is 20% - 21%.