The federal procurement system is built on a complex and comprehensive set of rules, regulations and case law for the protection of the taxpayers. These rules and regulations are meant to be enforced. Government contracts are contracts of adhesion in which the federal government dictates the terms and conditions. The contracts all contain special clauses permitting claims. Unlike the commercial world, contractors are meant to act as private attorneys general in policing the source selection process through bid protests. You are not in Kansas anymore. The federal procurement system invites you -- encourages you -- to protest and seek relief through claims. Since the playing field is tilted in the government's direction by law (taxpayer fiat), the procurement system affords contractors a way to even the field by protests and claims.
Therefore, contractors are not to be penalized for their actions in availing themselves of the relief afforded them. But don't just take my word for it. Listen carefully to the words written to all agency senior procurement executives (meant to be passed down) from the Administrator of the Office of Procurement Policy:
While many agencies and contractors have successfully resolved contentious contract issues by effectively using a wide range of dispute resolution techniques, concerns have arisen regarding the consideration federal agencies give contractor protests, claims and ADR practices in past performance evaluations and source selection decisions. For the reasons stated below, the filing of protests, the filing of claims, or the use of ADR, must not be considered by an agency in either past performance evaluations or source selection decisions. (Emphasis added.)The memorandum from OFPP goes on to state "contractors should feel free to avail themselves of the rights provided to them by law." The rights. Contractors are not to be downgraded for availing themselves of these rights when they file protests or claims and they may not be given positive past performance evaluations for refraining from filing protests or claims.
Government policy recognizes contractors' rights to avail themselves of remedies built into the system. Moreover, it is the policy of the executive branch of the federal government to not penalize contractors for exercising these rights or rewarding them for not doing so. The judicial branch certainly recognizes these principles as well, to say nothing of the legislative branch that enacted the very system which creates the rights. GAO bid protest decisions support this policy. We can provide you the case citations.
Let me know if this policy is not being practiced at the working level or if you want a copy of the OFPP memorandum (or citation to the GAO decisions).