PAGE purification is recommended for oligos of this length not only because truncations occur but because single base deletions may occur anywhere along the length of the oligo. Oligo synthesis efficiency is ~99% efficient at each cycle of chemistry. This means that deletion events may occur at each and every position. These undesired truncation/deletion products accumulate as the oligo elongates, so long oligos will be more affected by this problem than short oligos. For a 97nt oligo, ~60% of the product made will be these truncation products. It is possible that a deletion mutant my occur in your restriction site, which would decrease the efficiency of the enzyme cutting and therefore preventing the oligo from being cloned into your vector efficiently. For more details, please review our Technical Reports
on Oligonucleotide Synthesis and Oligonucleotide Purification.