Using short tags is discouraged because they are in conflict with XML's open tag (<?xml). If the file is actually XML, the PHP interpreter will process everything after the <? as PHP code, resulting in a parsing error.
Another reason to always use full PHP opening tags is to avoid the unknown. For example, a hosting provider that doesn't allow short open tags (<? ?>) on their servers.
Testing older scripts
For testing older scripts, you can switch short open tags on temporarily. After testing, be sure to switch short form open tags off and retest the scripts.
Converting older scripts
Replace all occurrences of <? ?> with <?php ?>
There's a similar issue with ASP-like <% %> tags. The Uniform Server Zero default is asp_tags = Off