I would go along with one point Subash mentioned, namely no. 4. It is very advisable to bear in mind that available media can cause contaminations, even if bought from specialist companies. You can never be completely sure, whether the production was as sterile as it sholud be. I assume you check your filters regularly, thus it may not be the problem. If not though, this can be a reason as well.

If you are working using a laminar flow cabinet you shall also remember to sterilize it with UV light (at least half an hour in advance) and  wash it with ehanol. You can also leave the UV light turned on in the laboratory during the night before the experiment.

Also, it would be good if you were able to find out whether there is another experiment being carried out simultaneously to the one of yours, as any clear medium you use is prone to be inhabited by microorganisms. The environment of fresh medium is very attractive for almost all the microorganisms.

You mentioned you autoclave all the spare parts etc., however, assuming there is another experiment going on in the laboratory you conduct your tests you have to be very careful when handling with the equipment after the autoclaving process.

Keeping positive pressure inside the bioreactor system may help minimize the contamination issues.

The general environment in which the fermentation is being performed may be suspect since the media reservoir becomes contaminated.  In this regard, this speaks to previous answers regarding "other" expt.   In theory, the media reservoir would be would be the easiest to sterilize.  However when the media is "pumped" out, or exits the reservoir,  gas a has to enter the reservoir so in general negative pressure exists in the reservoir.  You have to look at how the "venting" system is set-up.  Simple filter vents won't block many spores since 0.2um "sterilization" will pass many spores.   Without knowing specifics, its hard to say so you have to break down the system to isolate the source.  If you are using vent-filters, don't try to reuse them since non-uniform temperature gradients won't kill spores trapped in the filter.  Also prolonged heat sterilization would only served to accelerate the thermal decomposition of the filter material over time.

What you are doing to avoid contamination is perfectly right. However, you need to examine certain gaps in your bioreactor where there is always a chance of steam condensate accumulating and that is the source of contamination.  I do not know the bioreactor design which you are using and hence it is upto you to search for such critical control points.

Besides all comments posted, maybe your scaffold sterilization system is not appropiate. Try to irradiate the scaffold 25 - 30 KGray instead of using steam for ensure sterility.

Thanks all for your answers..They have helped me a lot in realising where i could be going wrong..will get back after trying out these some of the suggestions..do keep posting suggestions..once again..thanks :)