The issue is you're not using things correctly. You should never call blocks directly from templates. Use regions in templates and add blocks to them from GUI, or you can expect IDs to get messed up.

If you need to place a block in two places, see answers to [Place a block in multiple regions][2] question. Or, if it's a Views block, simply clone block display.

To reliably style a block, you can use [Block Class][1] module to assign a class that will not change.


----------

Note that not only IDs will get messed up when you call block directly, but also things like permissions and cache settings may get compromised.

  [1]: https://drupal.org/project/block_class
  [2]: http://drupal.stackexchange.com/q/9677/16495