Comment 1 for bug 412116

Fixed in 0.47, see Release notes/0.47 > Notable bug fixes:
"No more ID clashes on import and paste: previously, importing or pasting SVG objects might sometimes distort their colors, because the imported objects referred to gradients with the same IDs as those that already exist in the document but look different. Now, IDs of all gradients in the pasted document are checked for clashes with those in the host document, and if necessary changed with all their users updated correspondingly, so such unexpected color changes will never happen. "
<http://wiki.inkscape.org/wiki/index.php/Release_notes/0.47#Notable_bug_fixes>

Could you test with a recent prerelease build from <http://sourceforge.net/projects/inkscape/files/> if this issue still persists?