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Hey Kero,
It sounds like mold in the fruit fly cultures. Once that forms it is very hard to get flies. I get it in a percentage of my culture as well, so I don't have a solution for you. Just make more cultures from any "good" ones. I don't know what culture media you are using, but maybe try using a mix of vinegar and water as opposed to just water, it helps.
As for the flour beetles, the ADZR way is one alternative. I also have 2 strainers the one with tiny holes and one that lets almost all the buggers get through. I can tell you from experience that the smaller strainer lets very tiny larvae and eggs get through. Your best bet is to do this little trick and you will have an easy time of the beetles.

Strain your entire culture with the small strainer and use the adults and larvae to start another culture. With the sifted flour there will be eggs and small larvae. In ONE week strain the flour/first culture. You will find it teeming with larvae. I use the larger strainer so that I only get the larger larvae. You can keep doing this for about a month. After a month strain the second culture and you can either start culture number 3 or put the adults and larvae back into culture number 1. I think you can re-use the flour for about 3-4 times. An even better description of this is at:

http://doylesdartden.com/flourbeetles.html

Hope this helps.

-Ben
 

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You could use it more often, but you will lose production of larvae, so you will want to replace it. If you do get 3-4 uses that is 6 - 9 months or so. That is way cheaper than FF cultures. Also you don't have to use the shoebox containers. I use the 32oz deli cups with a paper towel over the top to keep the adults in. They are only half to 3/4 filled with flour.

-Ben
 
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