There is a known limitation in Windows Search that is supplied with Windows Server 2008. Depending on the density of the text, large text documents (for example a 200+ page Adobe PDF file) may not be completely indexed for full-text searches. The indexing is truncated when the maximum word count per document is reached. Smaller documents are indexed completely.
If your vault will contain such documents and full-text search is an important feature for you, we have two recommendations: