Error  "Email confirmation doesn't match given email address error"
comes from 'emailverificationwrong' translation token.
flyspray-1.0-rc10/includes>grep -rin2 emailverificationwrong .
./modify.inc.php-909-
./modify.inc.php-910-        if ($fs->prefs['repeat_emailaddress'] && trim(Post::val('email_address')) != trim(Post::val('verify_email_address'))) {
./modify.inc.php:911:            Flyspray::show_error(L('emailverificationwrong'));
./modify.inc.php-912-            break;
./modify.inc.php-913-        }
--
--
./modify.inc.php-1133-        
./modify.inc.php-1134-        if ($fs->prefs['repeat_emailaddress'] && $email != trim(Post::val('verify_email_address'))) {
./modify.inc.php:1135:            Flyspray::show_error(L('emailverificationwrong'));
./modify.inc.php-1136-            break;
./modify.inc.php-1137-        }
So maybe there is repeat_emailaddress set to 1(true), but you are using an older but not the default 'CleanFS'-template that shows the second email input in the form if setting repeat_emailaddress is set.
So I suggest either adapt the template you use to contain the 'verify_email_address' input as in the CleanFS-templates:
./themes/CleanFS/templates/common.newuser.tpl-48-    <?php if( $do==='register' && $fs->prefs['repeat_emailaddress'] ): ?>
./themes/CleanFS/templates/common.newuser.tpl-49-        <li>
./themes/CleanFS/templates/common.newuser.tpl-50-            <label for="verifyemailaddress"><?= eL('verifyemailaddress') ?></label>
./themes/CleanFS/templates/common.newuser.tpl:51:            <input id="verifyemailaddress" value="<?php echo Filters::noXSS(Req::val('verify_email_address')); ?>" name="verify_email_address" required="required" type="text" size="20" maxlength="100" />
./themes/CleanFS/templates/common.newuser.tpl-52-        </li>
./themes/CleanFS/templates/common.newuser.tpl-53-    <?php endif; ?>
./themes/CleanFS/templates/common.newuser.tpl-54-
--
--
./themes/CleanFS/templates/register.no-magic.tpl-26-        <?php if ($fs->prefs['repeat_emailaddress']): ?>
./themes/CleanFS/templates/register.no-magic.tpl-27-        <li>
./themes/CleanFS/templates/register.no-magic.tpl-28-            <label for="verifyemailaddress"><?= eL('verifyemailaddress') ?></label>
./themes/CleanFS/templates/register.no-magic.tpl:29:            <input id="verifyemailaddress" value="<?php echo Filters::noXSS(Req::val('verify_email_address')); ?>" name="verify_email_address" required="required" type="text" size="20" maxlength="100" />
./themes/CleanFS/templates/register.no-magic.tpl-30-        </li>
./themes/CleanFS/templates/register.no-magic.tpl-31-        <?php endif ?>
./themes/CleanFS/templates/register.no-magic.tpl-32-
 Or disable the repeat_emailaddress setting so that check is not used.