My family has a minhag to wait less time (3 hours as opposed to 6) between Meat and Milk on Shavuos. I was wondering if this has a written source?
[or if not, has anyone else heard of it?]
The Minchas Yaakov 76:5 quotes the Kol Bo that one may employ leniencies to fulfill the custom of eating milchigs after Mincha on Shavuos, when less than six hours have elapsed since the meat meal after Shacharis, provided one has cleaned his mouth from the meat between his teeth. Yet, he concludes that it is better not to do so.
In addition, the Poskim discuss the difference on Shavuos regarding waiting to eat meat after eating dairy. The Mishbetzos Zahav 89:3 writes that even according to those opinions that are stringent requiring a wait of one hour after eating dairy before eating meat, on Shavuos they agree that one may be lenient and finish the dairy meal, recite Birkas ha'Mazon, and begin the meat meal immediately afterwards.
The Noam Elimelech writes that "On Shavuos we are allowed to not wait after milk the normal amount of time [before eating meat]".
The Satmerer Rebbes (R' Yoel) said that one can drink milk in the morning after 5 hours from eating meat at night if he slept in between. R' Dov Berish from Biala said one can eat milk in the afternoon after 5 hours from his meat meal if he slept.
However, while the Chasam Sofer originally held of this opinion, he changed his mind after the cup of milk that he prepared from the night before broke.
The Sh'lo adds that one should be "particular, especially on a holy day like this, which is the day of the giving of our Torah, to clean and rinse one's mouth thoroughly, to 'interrupt' between the milchigs and meat meal with bircas hamozon and to wait an hour, and afterwards put on another table cloth and to set the table." http://www.chabadtalk.com/go/ph/ph-6.htm
German Jews would wait 3 hours between Meat and Milk all year round, not just Shavuos. (See page 2 of this issue of Halachically Speaking, and see footnote 15 for the reason according to Rav Belsky).
The Aruch Hashulchan says that if one has a custom to wait 6 hours, one dare not change it. (page 3)
However, this is talking about all year round, not Shavuos specifically.
See Gershon Gold's answer for some Shavuos specific leniencies.